Methods of treating hemophilia in patients having developed inhibitory antibodies

ABSTRACT

This invention relates to Factor VIII muteins that are covalently bound, at a predefined site that is not an N-terminal amine, to one or more biocompatible polymers such as polyethylene glycol. The mutein conjugates retain FVIII procoagulant activity and have improved pharmacokinetic properties.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.13/748,983 filed on Jan. 24, 2013, which is a continuation of U.S.patent application Ser. No. 12/540,703 filed on Aug. 13, 2009, which isa continuation of U.S. patent application Ser. No. 11/273,896 filed onNov. 14, 2005 (now U.S. Pat. No. 7,632,921), which claims benefit ofpriority to U.S. Patent App. Ser. No. 60/627,277 filed on Nov. 12, 2004,all of which applications are hereby incorporated herein by reference intheir entireties.

FIELD OF THE INVENTION

This invention relates to Factor VIII (FVIII) muteins that allowcoupling, at a defined site, to one or more biocompatible polymers suchas polyethylene glycol. In addition, related formulations, dosages andmethods of administration thereof for therapeutic purposes are provided.These modified FVIII variants, and associated compositions and methodsare useful in providing a treatment option with reduced injectionfrequency and reduced immunogenic response for individuals afflictedwith hemophilia A.

BACKGROUND OF THE INVENTION

Hemophilia A is the most common hereditary coagulation disorder, with anestimated incidence of 1 per 5000 males. It is caused by deficiency orstructural defects in FVIII, a critical component of the intrinsicpathway of blood coagulation. The current treatment for hemophilia Ainvolves intravenous injection of human FVIII. Human FVIII has beenproduced recombinantly as a single-chain molecule of approximately 300kD. It consists of the structural domains A1-A2-B-A3-C1-C2 (Thompson,2003, Semin. Hematol. 29, pp. 11-22). The precursor product is processedinto two polypeptide chains of 200 kD (heavy) and 80 kD (light) in theGolgi Apparatus, with the two chains held together by metal ions(Kaufman et al., 1988, J. Biol. Chem. 263, p. 6352; Andersson et al.,1986, Proc. Natl. Acad. Sci. 83, p. 2979).

The B-domain of FVIII seems to be dispensable as B-domain deleted FVIII(BDD, 90 kD A1-A2 heavy chain plus 80 kD light chain) has also beenshown to be effective as a replacement therapy for hemophilia A. TheB-domain deleted FVIII sequence contains a deletion of all but 14 aminoacids of the B-domain.

Hemophilia A patients are currently treated by intravenousadministration of FVIII on demand or as a prophylactic therapyadministered several times a week. For prophylactic treatment 15-25IU/kg bodyweight is given of factor VIII three times a week. It isconstantly required in the patient. Because of its short half-life inman, FVIII must be administered frequently. Despite its large size ofgreater than 300 kD for the full-length protein, FVIII has a half-lifein humans of only about 11 hours. (Ewenstein et al, 2004, Semin.Hematol. 41, pp. 1-16). The need for frequent intravenous injectioncreates tremendous barriers to patient compliance. It would be moreconvenient for the patients if a FVIII product could be developed thathad a longer half-life and therefore required less frequentadministration. Furthermore, the cost of treatment could be reduced ifthe half-life were increased because fewer dosages may then be required.

An additional disadvantage to the current therapy is that about 25-30%of patients develop antibodies that inhibit FVIII activity (Saenko etal, 2002, Haemophilia 8, pp. 1-11). The major epitopes of inhibitoryantibodies are located within the A2 domain at residues 484-508, the A3domain at residues 1811-1818, and the C2 domain. Antibody developmentprevents the use of FVIII as a replacement therapy, forcing this groupof patients to seek an even more expensive treatment with high-doserecombinant Factor Vila and immune tolerance therapy.

The following studies identified FVIII epitopes of inhibitoryantibodies. In a study of 25 inhibitory plasma samples, 11 were found tobind to the thrombin generated 73 kD light chain fragment A3C1C2, 4 tothe A2 domain, and 10 to both (Fulcher, C. et al., 1985, Proc. Natl.Acad. Sci. 2(22), pp. 7728-32). In another study, six of eight A2 domaininhibitors from patients were neutralized by a recombinant A2polypeptide (Scandella, D. et al., 1993, Blood 82(6), pp. 1767-75).Epitopes for six of nine inhibitors from patients were mapped to A2residues 379-538 (Scandella, D. et al., 1988, Proc. Natl. Acad. Sci.85(16), pp. 6152-6). An epitope for 18 heavy-chain inhibitors waslocalized to the same N-terminal 18.3 kD region of the A2 domain(Scandella, D. et al., 1989, Blood 74(5), pp. 1618-26).

An active, recombinant hybrid human/porcine FVIII molecule, generated byreplacing human A2 domain residues 387-604 with the homologous porcinesequence, was resistant to a patient A2 inhibitor (Lubin, I. et al.,1994, J. Biol. Chem. 269(12), pp. 8639-41) and resistant to a murinemonoclonal antibody mAB 413 IgG that competes with patient A2 inhibitorsfor binding to A2 (Scandella, D. et al., 1992, Thromb Haemost. 67(6),pp. 665-71). This A2 domain epitope was further localized to the A2domain residues 484-508 when experiments showed that mAB 413 IgG andfour patient inhibitors did not inhibit a hybrid human/porcine FVIII inwhich the A2 domain residues 484-508 were replaced with that of porcine(Healey, J. et al., 1995, J. Biol. Chem. 270(24), pp. 14505-9). Thishybrid FVIII was also more resistant to at least half of 23 patientplasmas screened (Barrow, R. et al., 2000, Blood 95(2), pp. 564-8).Alanine scanning mutagenesis identified residue 487 to be critical forbinding to all five patient inhibitors tested, while residues 484, 487,489, and 492 were all important to interaction with mAB 413 IgG (Lubin,I., J. Biol. Chem. 272(48), pp. 30191-5). Inhibitory antibody titers inmice receiving the R484A/R489A/P492A mutant, but not the R484A/R489Amutant, were significantly lower than in mice receiving control humanBDD FVIII (Parker, E. et al., 2004, Blood 104(3), pp. 704-10). In sum,the 484-508 region of the A2 domain seems to be a binding site forinhibitors of FVIII activity.

In addition to the development of an immune response to FVIII, anotherproblem with conventional therapy is that it requires frequent dosagingbecause of the short half-life of FVIII in vivo. The mechanisms forclearance of FVIII from the circulation have been studied.

FVIII clearance from circulation has been partly attributed to specificbinding to the low-density lipoprotein receptor-related protein (LRP), ahepatic clearance receptor with broad ligand specificity (Oldenburg etal., 2004, Haemophilia 10 Suppl 4, pp. 133-139). Recently, thelow-density lipoprotein (LDL) receptor was also shown to play a role inFVIII clearance, such as by cooperating with LRP in regulating plasmalevels of FVIII (Bovenschen et al., 2005, Blood 106, pp. 906-910). Bothinteractions are facilitated by binding to cell-surface heparin sulphateproteoglycans (HSPGs). Plasma half-life in mice can be prolonged by3.3-fold when LRP is blocked or 5.5-fold when both LRP and cell-surfaceHSPGs are blocked (Sarafanov et al., 2001, J. Biol. Chem. 276, pp.11970-11979). HSPGs are hypothesized to concentrate FVIII on the cellsurface and to present it to LRP. LRP binding sites on FVIII have beenlocalized to A2 residues 484-509 (Saenko et al., 1999, J. Biol. Chem.274, pp. 37685-37692), A3 residues 1811-1818 (Bovenschen et al., 2003,J. Biol. Chem. 278, pp. 9370-9377) and an epitope in the C2 domain(Lenting et al., 1999, J. Biol. Chem. 274, pp. 23734-23739).

FVIII is also cleared from circulation by the action of proteases. Tounderstand this effect, one must understand the mechanism by which FVIIIis involved in blood coagulation. FVIII circulates as a heterodimer ofheavy and light chains, bound to vWF. VWF binding involves FVIIIresidues 1649-1689 (Foster et al., 1988, J. Biol. Chem. 263, pp.5230-5234), and parts of C1 (Jacquemin et al., 2000, Blood 96, pp.958-965) and C2 domains (Spiegel, P. et al., 2004, J. Biol. Chem.279(51), pp. 53691-8). FVIII is activated by thrombin, which cleavespeptide bonds after residues 372, 740, and 1689 to generate aheterotrimer of A1, A2, and A3-C1-C2 domains (Pittman et al., 1988,Proc. Natl. Acad. Sci. 85, pp. 2429-2433). Upon activation, FVIIIdissociates from vWF and is concentrated to the cell surface ofplatelets by binding to phospholipid. Phospholipid binding involvesFVIII residues 2199, 2200, 2251, and 2252 (Gilbert et al., 2002, J.Biol. Chem. 277, pp. 6374-6381). There it binds to FIX throughinteractions with FVIII residues 558-565 (Fay et al., 1994, J. Biol.Chem. 269, pp. 20522-20527) and 1811-1818 (Lenting et al., 1996, J.Biol. Chem. 271, pp. 1935-1940) and FX through interactions with FVIIIresidues 349-372 (Nogami et al., 2004, J. Biol. Chem. 279, pp.15763-15771) and acts as a cofactor for FIX activation of FX, anessential component of the intrinsic coagulation pathway. ActivatedFVIII (FVIIIa) is partly inactivated by the protease activated protein C(APC) through cleavage after FVIII residues 336 and 562 (Regan et al.,1996, J. Biol. Chem. 271, pp. 3982-3987). The predominant determinant ofinactivation, however, is the dissociation of the A2 domain from A1 andA3-C1-C2 (Fay et al., 1991, J. Biol. Chem. 266, pp. 8957-8962).

One method that has been demonstrated to increase the in vivo half-lifeof a protein is PEGylation. PEGylation is the covalent attachment oflong-chained polyethylene glycol (PEG) molecules to a protein or othermolecule. The PEG can be in a linear form or in branched form to producedifferent molecules with different features. Besides increasing thehalf-life of peptides or proteins, PEGylation has been used to reduceantibody development, protect the protein from protease digestion andkeep the material out of the kidney filtrate (Harris et al., 2001,Clinical Pharmacokinetics 40, pp. 539-51). In addition, PEGylation mayalso increase the overall stability and solubility of the protein.Finally, the sustained plasma concentration of PEGylated proteins canreduce the extent of adverse side effects by reducing the trough to peaklevels of a drug, thus eliminating the need to introducesuper-physiological levels of protein at early time-points.

Random modification of FVIII by targeting primary amines (N-terminus andlysines) with large polymers such as PEG and dextran has been attemptedwith varying degree of success (WO94/15625, U.S. Pat. No. 4,970,300,U.S. Pat. No. 6,048,720). The most dramatic improvement, published in a1994 patent application (WO94/15625), shows a 4-fold half-lifeimprovement but at a cost of 2-fold activity loss after reactingfull-length FVIII with 50-fold molar excess of PEG. WO2004/075923discloses conjugates of FVIII and polyethylene glycol that are createdthrough random modification. Randomly PEGylated proteins, such asinterferon-alpha (Kozlowski et al, 2001, BioDrugs 15, pp. 419-429) havebeen approved as therapeutics in the past.

This random approach, however, is much more problematic for theheterodimeric FVIII. FVIII has hundreds of potential PEGylation sites,including the 158 lysines, the two N-termini, and multiple histidines,serines, threonines, and tyrosines, all of which could potentially bePEGylated with reagents primarily targeting primary amines. For example,the major positional isomer for PEGylated interferon Alpha-2b was shownto be a histidine (Wang et al., 2000, Biochemistry 39, pp. 10634-10640).Furthermore, heterogeneous processing of full length FVIII can lead to amixture of starting material that leads to further complexity in thePEGylated products. An additional drawback to not controlling the siteof PEGylation on FVIII is a potential activity reduction if the PEG wereto be attached at or near critical active sites, especially if more thanone PEG or a single large PEG is conjugated to FVIII. Because randomPEGylation will invariably produce large amounts of multiply PEGylatedproducts, purification to obtain only mono-PEGylated products willdrastically lower overall yield. Finally, the enormous heterogeneity inproduct profile will make consistent synthesis and characterization ofeach lot nearly impossible. Since good manufacturing requires aconsistent, well-characterized product, product heterogeneity is abarrier to commercialization. For all these reasons, a more specificmethod for PEGylating FVIII is desired.

Various site-directed protein PEGylation strategies have been summarizedin a recent review (Kochendoerfer, G., Curr. Opin. Chem. Biol. 2005,available online as of Oct. 15, 2005, direct object identifierdoi:10.1016/j.cbpa.2005.10.007). One approach involves incorporation ofan unnatural amino acid into proteins by chemical synthesis orrecombinant expression followed by the addition of a PEG derivative thatwill react specifically with the unnatural amino acid. For example, theunnatural amino acid may be one that contains a keto group not found innative proteins. However, chemical synthesis of proteins is not feasiblefor a protein as large as FVIII. Current limit of peptide synthesis isabout 50 residues. Several peptides can be ligated to form a largerpiece of polypeptide, but to produce even the B-domain deleted FVIIIwould require greater than 20 ligations, which would result in less than1% recovery even under ideal reaction condition. Recombinant expressionof proteins with unnatural amino acids has so far mainly been limited tonon-mammalian expression systems. This approach is expected to beproblematic for a large and complex protein such as FVIII that needs tobe expressed in mammalian systems.

Another approach to site-specific PEGylation of proteins is by targetingN-terminal backbone amine with PEG-aldehydes. The low pH required underthis process to achieve specificity over other amine groups, however, isnot compatible with the narrow near-neutral pH range needed for thestability of FVIII (Wang et al., 2003, International J. Pharmaceutics259, pp. 1-15). Moreover, N-terminal PEGylation of FVIII may not lead toimproved plasma half-life if this region is not involved in plasmaclearance. In fact, the N-terminal region of the FVIII light chain hasbeen implicated in binding to the von Willebrand factor (vWF), a carrierprotein that is critical for FVIII survival in circulation. ByN-terminal modification of factor VIII, the critically importantassociation with vWF may be disrupted or weakened. Thus, N-terminalPEGylation of FVIII may have the opposite effect of reducing plasmahalf-life of FVIII.

WO90/12874 discloses site-specific modification of human IL-3,granulocyte colony stimulating factor and erythropoietin polypeptides byinserting or substituting a cysteine for another amino acid, then addinga ligand that has a sulfhydryl reactive group. The ligand couplesselectively to cysteine residues. Modification of FVIII or any variantthereof is not disclosed.

For the reasons stated above, there exists a need for an improved FVIIIvariant that possesses greater duration of action in vivo and reducedimmunogenicity, while retaining functional activity. Furthermore, it isdesirable that such a protein be produced as a homogeneous product in aconsistent manner.

SUMMARY OF THE INVENTION

It is an object of the present invention to provide a biocompatiblepolymer-conjugated functional FVIII polypeptide having improvedpharmacokinetic characteristics and therapeutic characteristics.

It is another object of the present invention to provide a biocompatiblepolymer-conjugated B domain deleted FVIII protein having improvedpharmacokinetic properties.

It is yet another object of the invention to provide a biocompatiblepolymer-conjugated functional FVIII polypeptide having reduced bindingto the low-density lipoprotein receptor-related protein (LRP),low-density lipoprotein (LDL) receptor, the heparan sulphateproteoglycans (HSPGs) and/or inhibitory antibodies against FVIII.

It is yet another object of the present invention to provide an improvedFVIII variant that possesses greater duration of action in vivo andreduced immunogenicity, which is capable of being produced as ahomogeneous product in a consistent manner.

In one aspect of the invention there is provided a conjugate havingfactor VIII procoagulant activity comprising a functional factor VIIIpolypeptide covalently attached at one or more predefined sites on thepolypeptide to one or more biocompatible polymers, wherein thepredefined site is a not an N-terminal amine. The invention alsoincludes a method for the preparation of this conjugate comprisingmutating a nucleotide sequence that encodes for the functional factorVIII polypeptide to substitute a coding sequence for a cysteine residueat a pre-defined site; expressing the mutated nucleotide sequence toproduce a cysteine enhanced mutein; purifying the mutein; reacting themutein with the biocompatible polymer that has been activated to reactwith polypeptides substantially only at the introduced cysteine residuessuch that the conjugate is formed; and purifying the conjugate. Theinvention is also directed to pharmaceutical compositions comprising theconjugate and a pharmaceutically acceptable adjuvant and methods oftreating hemophilia by administering therapeutically effective amountsof these pharmaceutical compositions to a mammal in need thereof.

The invention also relates to a method for site-directed PEGylation of afactor VIII mutein comprising (a) expressing a site-directed factor VIIImutein wherein the mutein has a cysteine replacement for an amino acidresidue on the exposed surface of the factor VIII mutein and thatcysteine is capped; (b) contacting the cysteine mutein with a reductantunder conditions to mildly reduce the cysteine mutein and to release thecap; (c) removing the cap and the reductant from the cysteine mutein;and (d) at least about 5 minutes after the removal of the reductant,treating the cysteine mutein with PEG comprising a sulfhydryl couplingmoiety under conditions such that PEGylated factor VIII mutein isproduced.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A-1B. Vector maps and mutagenesis strategy for PEG muteins. FIG.1A shows the Mutagenesis Vector and Shuttle Vector. FIG. 1B shows theExpression Vector.

FIG. 2. A UV absorbance profile at 280 nm with respect to time for thePEG2 protein purified over a monoclonal FVIII antibody chromatographycolumn. The chromatography was performed using an AKTA® Explorer 100chromatography system from Amersham Bioscience.

FIG. 3 Three-step site-directed PEGylation method. PEG represents acysteine-reactive PEG such as PEG-maleimide. Closed bars representdisulfide formation while open bars represent reduced cysteines.

FIG. 4. Site-directed PEGylation of PEG2.

FIG. 5. Site-directed PEGylation of PEG6.

FIG. 6A-6D. Site-directed PEGylation of BDD, PEG2, 4, 5, and 6. FIGS. 6Aand 6B were stained with heavy (H) chain antibody while FIGS. 6C and 6Dwere stained with light (L) chain antibody. “U” is unprocessed materialcontaining both H & L.

FIG. 6E. PEGylation of PEG15 and PEG7 with PEG2 and PEG6 as controls.Start purified PEG muteins (“S”) are reduced with TCEP and PEGylatedwith a 12 kD (“12”) or a 22 kD (“22”) PEG after removal of the reductant(“R”). Samples were run on 6% Tris-glycine SDS PAGE and stained with aheavy chain (“HC”) antibody on left panel or light chain (“LC”) antibodyon right panel. “U” is unprocessed material containing both HC & LC.PEGylated bands are highlighted by dots.

FIG. 6F. PEGylation of PEG2+6 with PEG2 and PEG6 as controls. PEG2,PEG6, or PEG2+6 is reduced with TCEP and PEGylated with a 5 kD (“5”) ora 43 kD (“43”) PEG after removal of the reductant (“R”). PEG2+6 was alsoPEGylated with 12, 22, and 33 kD PEGs. Samples were run on 6%Tris-glycine SDS PAGE and stained with coomassie for proteins on theleft or heavy chain (H) or light chain (L) antibody. “U” is unprocessedmaterial containing both H & L. PEGylated bands are highlighted by dots.

FIG. 6G. PEGylation of wildtype full length FVIII (KG-2) with PEG2 as acontrol. Left gel stained with coomassie stain for proteins and rightgel with iodine for PEG. “BDD U” is unprocessed BDD material containingboth H & L. PEGylated bands are highlighted by dots.

FIG. 7. Thrombin cleavage of PEGylated PEG2. The N-terminal half of A2domain is colored in blue and C-terminal half in green, with the R8B12antibody epitope highlighted in dark green (right FVIII model). PEG2(lane 1) and 22 kD PEGylated PEG2 (lane2) were treated with thrombin(lanes 3 and 4, respectively) and then run on a 7% Tris-Acetate gel(Invitrogen) and stained with the R8B12 antibody. Each lane containsabout 50 ng of FVIII.

FIG. 8. Thrombin cleavage of PEGylated wildtype full-length FVIII(KG-2). “S”=starting KG-2 material. “R”=reduced KG-2 and reductantremoved. “P”=“R” PEGylated with 43 kD PEG. “Pure”=“P” purified away fromexcess PEG. “L”=light chain. PEGylated bands are highlighted by dots.

FIG. 9. Iodine Staining of PEGylated PEG2. 22 or 43 kD PEGylated PEG2was run on a 6% TrisGlycine gel and stained with the R8B12 FVIIIantibody (lanes 1 and 2) or iodine (lanes 3 and 4). The two stains werelined up according to their molecular weight marker lanes. Lanes 1 and 2each contains about 30 ng of FVIII while lanes 3 and 4 contain about 2μg.

FIG. 10A-10B. MALDI Mass Spectrometry analysis of PEGylated andUnPEGylated PEG2. MALDI Mass Spectrometry was performed on PEG2 (FIG.10A) or 22 kD PEGylated PEG2 (FIG. 10B). Upon PEGylation, the heavy (H)chain peak of PEG2 is greatly reduced and a new peak (H+PEG), centeredat 111 kD (22 kD PEG+89 kD heavy chain), appears. No PEGylated light (L)chain peak, expected to be centered at 100 kD (22 kD PEG+83 kD lightchain) is detected.

FIG. 11A-11B. MALDI Mass Spectrometry of PEGylated and unPEGylated PEG2after thrombin cleavage.

FIG. 12A-12D. MALDI Mass Spectrometry analysis of PEGylated PEG6 beforeand after thrombin cleavage.

FIG. 13. The UV absorption profile at 280 nm of PEGylated PEG2 purifiedon size-exclusion column.

FIG. 14. The UV absorption profile at 280 nm of PEGylated andUnPEGylated PEG6 purified on cation exchange column.

FIG. 15. The UV absorption profile at 280 nm of PEGylated andUnPEGylated PEG6 purified on size-exclusion column.

FIG. 16. Activity of PEGylated protein is compared to activity of theunPEGylated protein as measured by a chromogenic assay and a coagulationassay. Purified full-length FVIII is represented as KG-2. The percentactivity reported was determined by dividing the value of sample treatedwith PEG after reduction and reductant removal by that of the sampletreated with buffer control taking into consideration the PEGylationyield.

FIG. 17. Rabbit PK study of PEGylated PEG2 compared to PEG2.

FIG. 18. Rabbit PK study of PEGylated PEG2 compared to BDD and PEG2.P-values are comparisons between PEGylated PEG2 and BDD.

FIG. 19. Rabbit PK study of PEGylated PEG6 compared to BDD and PEG6.

FIG. 20. Rabbit PK study of PEGylated wildtype full-length (“fl”) FVIIIcompared to unmodified fl FVIII.

FIG. 21. Hemophilic mouse PK study of PEGylated PEG6 compared to PEG6and BDD.

FIG. 22. Normal mouse PK study of 22 and 43 kD PEGylated PEG2 comparedto BDD.

FIG. 23. Normal mouse PK study of 22 kD PEGylated PEG2 compared to BDD,full time course.

FIG. 24. The Hemophilic Mouse (BDD) Factor VIII recovery histogramdepicting a pharmacokinetic (PK) assessment of the half-life of twospecies of BDD Factor VIII in a hemophilic mouse assay.

FIG. 25. Hemophilic mouse kidney laceration study of 22 kD PEGylatedPEG2 compared to BDD. Vehicle treated mice have a blood loss of 25uL/gram body weight.

FIG. 26. Chromogenic Activity of PEGylated PEG2 and BDD in the presenceof increasing amounts of FVIII antibodies. Antibody epitope is denotedin parenthesis.

FIG. 27. Chromogenic Activity of PEGylated PEG2 in the presence ofincreasing amounts of FVIII mAB 413 antibodies.

FIG. 28A-28D. Chromogenic activity of BDD, 43 kD PEGylated PEG2, 33 kDPEGylated PEG6, and 33 kD diPEGylated PEG2+6 in the presence of humanplasma derived from patients that have developed inhibitors to FVIII.The inhibitor titer and date of blood collection were noted at the top.FIGS. 28A and 28B include data collected at patient plasma dilution of5- to 405-fold. FIG. 28C focuses on 1:15-fold dilution for patientHRF-828 plasma. FIG. 28D confirms that the 0.064 IU/mL used for eachFVIII sample in the top two panels was not a saturating dose.

FIG. 29. PEGylation screening method and validation. Top panel shows aschematic of PEGylation screening of transiently expressed PEG muteins.Bottom panel shows a Western analysis of PEGylated products using aheavy chain (“H”)-specific antibody (left) or a light-chain (“L”)specific antibody (right). PEGylated bands are highlighted by dots. “U”is unprocessed material containing both H and L.

FIG. 30. PEGylation screening of PEG15-17. Western analysis of PEGylatedproducts using heavy chain (“H”)-specific antibodies (R8B12 and 58.12)or light-chain (“L”) specific antibodies (C7F7 and GM). All 3 muteinsare selective for the heavy chain, with relative PEGylation efficiencyof PEG15-PEG16>PEG17. PEGylated bands are highlighted by dots. “U” isunprocessed material containing both H and L.

FIG. 31. Gel showing PEGylation of PEG2+14 as a function of reductantconcentration. PEG2+14 was treated with 67 to 670 uM of TCEP for 30minutes at 4° C. The reductant was removed by spin-column followed byPEGylation with a 12 kD PEG. Heavy and light chains of FVIII arehighlighted by “H” and “L,” respectively. The two dots point to thePEGylated heavy and light chains.

FIG. 32A-32F. Deconvoluted Mass Spectra of PEG2+14 treated with 67 to670 uM of TCEP followed by reductant removal. FIG. 32A shows PEG2+14;FIG. 32B shows reduction with 200 uM TCEP; FIG. 32C shows reduction with67 uM TCEP; FIG. 32D shows reduction with 400 uM TCEP; FIG. 32E showsreduction with 100 uM TCEP; and FIG. 32F shows reduction with 670 uMTCEP.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based on the discovery that polypeptides havingFVIII activity can be covalently attached at a predefined site to abiocompatible polymer that is not at an N-terminal amine, and that suchpolypeptides substantially retain their coagulant activity. Furthermore,these polypeptide conjugates have improved circulation time and reducedantigenicity. The conjugates of the invention are advantageous over theprior art conjugates that had random polymer attachments to FVIII orattachments at an N-terminal. Site-directed attachment allows one todesign modifications that avoid the regions required for biologicalactivity and thereby to maintain substantial FVIII activity. It alsoallows for designing to attach polymers to block binding at sitesinvolved in FVIII clearance. Site-directed attachment also allows for auniform product rather than the heterogeneous conjugates produced in theart by random polymer coupling. By avoiding attachment at an N-terminalamine of the light chain, the conjugates of the present invention avoidthe possible loss of activity from attaching a ligand at an active siteof the FVIII polypeptide. The N-terminal region of the light chain isbelieved to be involved in the association of vWF factor to FVIII, whichis a stabilizing association in the circulation.

DEFINITIONS

Biocompatible polymer. A biocompatible polymer includes polyalkyleneoxides such as without limitation polyethylene glycol (PEG), dextrans,colominic acids or other carbohydrate based polymers, polymers of aminoacids, biotin derivatives, polyvinyl alcohol (PVA), polycarboxylates,polyvinylpyrrolidone, polyethylene-co-maleic acid anhydride,polystyrene-co-malic acid anhydride, polyoxazoline,polyacryloylmorpholine, heparin, albumin, celluloses, hydrolysates ofchitosan, starches such as hydroxyethyl-starches and hydroxypropyl-starches, glycogen, agaroses and derivatives thereof, guar gum,pullulan, inulin, xanthan gum, carrageenan, pectin, alginic acidhydrolysates, other bio-polymers and any equivalents thereof. Preferredis polyethylene glycol, and still more preferred is methoxypolyethyleneglycol (mPEG). Other useful polyalkylene glycol compounds arepolypropylene glycols (PPG), polybutylene glycols (PBG), PEG-glycidylethers (Epox-PEG), PEG-oxycarbonylimidazole (CDI-PEG), branchedpolyethylene glycols, linear polyethylene glycols, forked polyethyleneglycols and multi-armed or “super branched” polyethylene glycols(star-PEG).

Polyethylene glycol (PEG). “PEG” and “polyethylene glycol” as usedherein are interchangeable and include any water-soluble poly(ethyleneoxide). Typically, PEGs for use in accordance with the inventioncomprise the following structure “—(OCH₂CH₂)_(n)—” where (n) is 2 to4000. As used herein, PEG also includes “—CH₂CH₂—O(CH₂CH₂O)_(n)—CH₂CH₂—”and “—(OCH₂CH₂)_(n)O—,” depending upon whether or not the terminaloxygens have been displaced. Throughout the specification and claims, itshould be remembered that the term “PEG” includes structures havingvarious terminal or “end capping” groups, such as without limitation ahydroxyl or a C₁₋₂₀ alkoxy group. The term “PEG” also means a polymerthat contains a majority, that is to say, greater than 50%, of —OCH₂CH₂—repeating subunits. With respect to specific forms, the PEG can take anynumber of a variety of molecular weights, as well as structures orgeometries such as branched, linear, forked, and multifunctional.

PEGylation. PEGylation is a process whereby a polyethylene glycol (PEG)is covalently attached to a molecule such as a protein.

Activated or Active functional group. When a functional group such as abiocompatible polymer is described as activated, the functional groupreacts readily with an electrophile or a nucleophile on anothermolecule.

B domain deleted FVIII (BDD). As used herein, BDD is characterized byhaving the amino acid sequence which contains a deletion of all but 14amino acids of the B-domain of FVIII. The first 4 amino acids of theB-domain (SFSQ, SEQ ID NO:1) are linked to the 10 last residues of theB-domain (NPPVLKRHQR, SEQ ID NO:2). (Lind, P. et al, 1995, Eur. J.Biochem. 232, pp. 19-27). The BDD used herein has the amino acidsequence of SEQ ID NO:3.

FVIII. Blood clotting Factor VIII (FVIII) is a glycoprotein synthesizedand released into the bloodstream by the liver. In the circulatingblood, it is bound to von Willebrand factor (vWF, also known as FactorVIII-related antigen) to form a stable complex. Upon activation bythrombin, it dissociates from the complex to interact with otherclotting factors in the coagulation cascade, which eventually leads tothe formation of a thrombus. Human full-length FVIII has the amino acidsequence of SEQ ID NO:4, although allelic variants are possible.

Functional factor VIII polypeptide. As used herein, functional factorVIII polypeptide denotes a functional polypeptide or combination ofpolypeptides that are capable, in vivo or in vitro, of correcting humanfactor VIII deficiencies, characterized, for example, by hemophilia A.Factor VIII has multiple degradation or processed forms in the naturalstate. These are proteolytically derived from a precursor, one chainprotein, as demonstrated herein. A functional factor VIII polypeptideincludes such single chain protein and also provides for these variousdegradation products that have the biological activity of correctinghuman factor VIII deficiencies. Allelic variations likely exist. Thefunctional factor VIII polypeptides include all such allelic variations,glycosylated versions, modifications and fragments resulting inderivatives of factor VIII so long as they contain the functionalsegment of human factor VIII and the essential, characteristic humanfactor VIII functional activity remains unaffected in kind. Thosederivatives of factor VIII possessing the requisite functional activitycan readily be identified by straightforward in vitro tests describedherein. Furthermore, functional factor VIII polypeptide is capable ofcatalyzing the conversion of factor X to Xa in the presence of factorIXa, calcium, and phospholipid, as well as correcting the coagulationdefect in plasma derived from hemophilia A affected individuals. Fromthe disclosure of the sequence of the human factor VIII amino acidsequences and the functional regions herein, the fragments that can bederived via restriction enzyme cutting of the DNA or proteolytic orother degradation of human factor VIII protein will be apparent to thoseskilled in the art.

FIX. As used herein, FIX means Coagulation Factor IX, which is alsoknown as Human Clotting Factor IX, or Plasma Thromboplastin Component.

FX. As used herein, FX means Coagulation Factor X, which is also knownby the names Human Clotting Factor X and by the eponym Stuart-Prowerfactor.

Pharmacokinetics. “Pharmacokinetics” (“PK”) is a term used to describethe properties of absorption, distribution, metabolism, and eliminationof a drug in a body. An improvement to a drug's pharmacokinetics meansan improvement in those characteristics that make the drug moreeffective in vivo as a therapeutic agent, especially its useful durationin the body.

Mutein. A mutein is a genetically engineered protein arising as a resultof a laboratory induced mutation to a protein or polypeptide.

Protein. As used herein, protein and polypeptide are synonyms.

FVIII clearance receptor. A FVIII clearance receptor as used hereinmeans a receptor region on a functional FVIII polypeptide that binds orassociates with one or more other molecules to result in FVIII clearancefrom the circulation. Factor VIII clearance receptors include withoutlimitation the regions of the FVIII molecule that bind LRP, LDL receptorand/or HSPG.

DISCUSSION

It is envisioned that any functional factor VIII polypeptide may bemutated at a predetermined site and then covalently attached at thatsite to a biocompatible polymer according to the methods of theinvention. Useful polypeptides include, without limitation, full-lengthfactor VIII having the amino acid sequence as shown in SEQ ID NO:4 andBDD FVIII having the amino acid sequence as shown in SEQ ID NO:3.Preferred is BDD FVIII.

The biocompatible polymer used in the conjugates of the invention may beany of the polymers discussed above. The biocompatible polymer isselected to provide the desired improvement in pharmacokinetics. Forexample, the identity, size and structure of the polymer is selected soas to improve the circulation half-life of the polypeptide having FVIIIactivity or decrease the antigenicity of the polypeptide without anunacceptable decrease in activity. Preferably, the polymer comprisesPEG, and still more preferably has at least 50% of its molecular weightas PEG. In one embodiment, the polymer is a polyethylene glycolterminally capped with an end-capping moiety such as hydroxyl, alkoxy,substituted alkoxy, alkenoxy, substituted alkenoxy, alkynoxy,substituted alkynoxy, aryloxy and substituted aryloxy. Still morepreferred are polymers comprising methoxypolyethylene glycol. Yet morepreferred are polymers comprising methoxypolyethylene glycol having asize range from 3 kD to 100 kD, and more preferably from 5 kD to 64 kDor from 5 kD to 43 kD.

Preferably the polymer has a reactive moiety. For example, in oneembodiment, the polymer has a sulfhydryl reactive moiety that can reactwith a free cysteine on a functional factor VIII polypeptide to form acovalent linkage. Such sulfhydryl reactive moieties include thiol,triflate, tresylate, aziridine, oxirane, S-pyridyl or maleimidemoieties. Preferred is a maleimide moiety. In one embodiment, thepolymer is linear and has a “cap” at one terminus that is not stronglyreactive towards sulfhydryls (such as methoxy) and a sulfhydryl reactivemoiety at the other terminus. In a preferred embodiment, the conjugatecomprises PEG-maleimide and has a size range from 5 kD to 64 kD.

Further guidance for selecting useful biocompatible polymers is providedin the examples that follow.

Site-directed mutation of a nucleotide sequence encoding polypeptidehaving FVIII activity may occur by any method known in the art.Preferred methods include mutagenesis to introduce a cysteine codon atthe site chosen for covalent attachment of the polymer. This may beaccomplished using a commercially available site-directed mutagenesiskit such as the Stratagene cQuickChange™ II site-directed mutagenesiskit, the Clontech Transformer site-directed mutagenesis kit no. K1600-1,the Invitrogen GenTaylor site-directed mutagenesis system no. 12397014,the Promega Altered Sites II in vitro mutagenesis system kit no. Q6210,or the Takara Mirus Bio LA PCR mutagenesis kit no. TAK RR016.

The conjugates of the invention may be prepared by first replacing thecodon for one or more amino acids on the surface of the functional FVIIIpolypeptide with a codon for cysteine, producing the cysteine mutein ina recombinant expression system, reacting the mutein with acysteine-specific polymer reagent, and purifying the mutein.

In this system, the addition of a polymer at the cysteine site can beaccomplished through a maleimide active functionality on the polymer.Examples of this technology are provided infra. The amount of sulfhydrylreactive polymer used should be at least equimolar to the molar amountof cysteines to be derivatized and preferably is present in excess.Preferably, at least a 5-fold molar excess of sulfhydryl reactivepolymer is used, and still more preferably at least a ten-fold excess ofsuch polymer is used. Other conditions useful for covalent attachmentare within the skill of those in the art.

In the examples that follow, the muteins are named in a mannerconventional in the art. The convention for naming mutants is based onthe amino acid sequence for the mature, full length Factor VIII asprovided in SEQ ID NO:4. As a secreted protein, FVIII contains a signalsequence that is proteolytically cleaved during the translation process.Following removal of the 19 amino acid signal sequence, the first aminoacid of the secreted FVIII product is an alanine.

As is conventional and used herein, when referring to mutated aminoacids in BDD FVIII, the mutated amino acid is designated by its positionin the sequence of full-length FVIII. For example, the PEG6 muteindiscussed below is designated K1808C because it changes the lysine (K)at the position analogous to 1808 in the full-length sequence tocysteine (C).

The predefined site for covalent binding of the polymer is best selectedfrom sites exposed on the surface of the polypeptide that are notinvolved in FVIII activity or involved in other mechanisms thatstabilize FVIII in vivo, such as binding to vWF. Such sites are alsobest selected from those sites known to be involved in mechanisms bywhich FVIII is deactivated or cleared from circulation. Selection ofthese sites is discussed in detail below. Preferred sites include anamino acid residue in or near a binding site for (a) low densitylipoprotein receptor related protein, (b) a heparin sulphateproteoglycan, (c) low density lipoprotein receptor and/or (d) factorVIII inhibitory antibodies. By “in or near a binding site” means aresidue that is sufficiently close to a binding site such that covalentattachment of a biocompatible polymer to the site would result in sterichindrance of the binding site. Such a site is expected to be within 20 Åof a binding site, for example.

In one embodiment of the invention, the biocompatible polymer iscovalently attached to the functional factor VIII polypeptide at anamino acid residue in or near (a) a factor VIII clearance receptor asdefined supra, (b) a binding site for a protease capable of degradationof factor VIII and/or (c) a binding site for factor VIII inhibitoryantibodies. The protease may be activated protein C (APC). In anotherembodiment, the biocompatible polymer is covalently attached at thepredefined site on the functional factor VIII polypeptide such thatbinding of low-density lipoprotein receptor related protein to thepolypeptide is less than to the polypeptide when it is not conjugated,and preferably more than twofold less. In one embodiment, thebiocompatible polymer is covalently attached at the predefined site onthe functional factor VIII polypeptide such that binding of heparinsulphate proteoglycans to the polypeptide is less than to thepolypeptide when it is not conjugated, and preferably is more thantwofold less. In a further embodiment, the biocompatible polymer iscovalently attached at the predefined site on the functional factor VIIIpolypeptide such that binding of factor VIII inhibitory antibodies tothe polypeptide is less than to the polypeptide when it is notconjugated, preferably more than twofold less than the binding to thepolypeptide when it is not conjugated. In another embodiment, thebiocompatible polymer is covalently attached at the predefined site onthe functional factor VIII polypeptide such that binding of low densitylipoprotein receptor to the polypeptide is less than to the polypeptidewhen it is not conjugated, preferably more than twofold less. In anotherembodiment, the biocompatible polymer is covalently attached at thepredefined site on the functional factor VIII polypeptide such that aplasma protease degrades the polypeptide less than when the polypeptideis not conjugated. In a further embodiment, the degradation of thepolypeptide by the plasma protease is more than twofold less than thedegradation of the polypeptide when it is not conjugated as measuredunder the same conditions over the same time period.

LRP, LDL receptor, or HSPG binding affinity for FVIII can be determinedusing surface plasmon resonance technology (Biacore). For example, FVIIIcan be coated directly or indirectly through a FVIII antibody to aBiacore™ chip, and varying concentrations of LRP can be passed over thechip to measure both on-rate and off-rate of the interaction (BovenschenN. et al., 2003, J. Biol. Chem. 278(11), pp. 9370-7). The ratio of thetwo rates gives a measure of affinity. A two-fold, preferably five-fold,more preferably ten-fold, and even more preferably 30-fold decrease inaffinity upon PEGylation would be desired.

Degradation of a FVIII by the protease APC can be measured by any of themethods known to those of skill in the art.

In one embodiment, the biocompatible polymer is covalently attached tothe polypeptide at one or more of the factor VIII amino acid positions81, 129, 377, 378, 468, 487, 491, 504, 556, 570, 711, 1648, 1795, 1796,1803, 1804, 1808, 1810, 1864, 1903, 1911, 2091, 2118 and 2284. Inanother embodiment, the biocompatible polymer is covalently attached tothe polypeptide at one or more of factor VIII amino acid positions 377,378, 468, 491, 504, 556, 1795, 1796, 1803, 1804, 1808, 1810, 1864, 1903,1911 and 2284 and (1) the binding of the conjugate to low-densitylipoprotein receptor related protein is less than the binding of theunconjugated polypeptide to the low-density lipoprotein receptor relatedprotein; (2) the binding of the conjugate to low-density lipoproteinreceptor is less than the binding of the unconjugated polypeptide to thelow-density lipoprotein receptor; or (3) the binding of the conjugate toboth low-density lipoprotein receptor related protein and low-densitylipoprotein receptor is less than the binding of the unconjugatedpolypeptide to the low-density lipoprotein receptor related protein andthe low-density lipoprotein receptor.

In a further embodiment, the biocompatible polymer is covalentlyattached to the polypeptide at one or more of factor VIII amino acidpositions 377, 378, 468, 491, 504, 556 and 711 and the binding of theconjugate to heparin sulphate proteoglycan is less than the binding ofthe unconjugated polypeptide to heparin sulphate proteoglycan. In afurther embodiment, the biocompatible polymer is covalently attached tothe polypeptide at one or more of the factor VIII amino acid positions81, 129, 377, 378, 468, 487, 491, 504, 556, 570, 711, 1648, 1795, 1796,1803, 1804, 1808, 1810, 1864, 1903, 1911, 2091, 2118 and 2284 and theconjugate has less binding to factor VIII inhibitory antibodies than theunconjugated polypeptide. In a further embodiment, the biocompatiblepolymer is covalently attached to the polypeptide at one or more of thefactor VIII amino acid positions 81, 129, 377, 378, 468, 487, 491, 504,556, 570, 711, 1648, 1795, 1796, 1803, 1804, 1808, 1810, 1864, 1903,1911, 2091, 2118 and 2284, and preferably at one or more of positions377, 378, 468, 491, 504, 556, and 711 and the conjugate has lessdegradation from a plasma protease capable of factor VIII degradationthan does the unconjugated polypeptide. More preferred, the plasmaprotease is activated protein C.

In a further embodiment, the biocompatible polymer is covalentlyattached to B-domain deleted factor VIII at amino acid position 129,491, 1804, and/or 1808, more preferably at 491 or 1808. In a furtherembodiment, the biocompatible polymer is attached to the polypeptide atfactor VIII amino acid position 1804 and comprises polyethylene glycol.Preferably, the one or more predefined sites for biocompatible polymerattachment are controlled by site specific cysteine mutation.

One or more sites, preferably one or two, on the functional factor VIIIpolypeptide may be the predefined sites for polymer attachment. Inparticular embodiments, the polypeptide is mono-PEGylated ordiPEGylated.

The invention also relates to a method for the preparation of theconjugate comprising mutating a nucleotide sequence that encodes for thefunctional factor VIII polypeptide to substitute a coding sequence for acysteine residue at a pre-defined site; expressing the mutatednucleotide sequence to produce a cysteine enhanced mutein; purifying themutein; reacting the mutein with the biocompatible polymer that has beenactivated to react with polypeptides at substantially only reducedcysteine residues such that the conjugate is formed; and purifying theconjugate. In another embodiment, the invention provides a method forsite-directed PEGylation of a factor VIII mutein comprising: (a)expressing a site-directed factor VIII mutein wherein the mutein has acysteine replacement for an amino acid residue on the exposed surface ofthe factor VIII mutein and that cysteine is capped; (b) contacting thecysteine mutein with a reductant under conditions to mildly reduce thecysteine mutein and to release the cap; (c) removing the cap and thereductant from the cysteine mutein; and (d) at least about 5 minutes,and preferably at least 15 minutes, still more preferably at least 30minutes after the removal of the reductant, treating the cysteine muteinwith PEG comprising a sulfhydryl coupling moiety under conditions suchthat PEGylated factor VIII mutein is produced. The sulfhydryl couplingmoiety of the PEG is selected from the group consisting of thiol,triflate, tresylate, aziridine, oxirane, S-pyridyl and maleimidemoieties, preferably maleimide.

The invention also concerns pharmaceutical compositions for parenteraladministration comprising therapeutically effective amounts of theconjugates of the invention and a pharmaceutically acceptable adjuvant.Pharmaceutically acceptable adjuvants are substances that may be addedto the active ingredient to help formulate or stabilize the preparationand cause no significant adverse toxicological effects to the patient.Examples of such adjuvants are well known to those skilled in the artand include water, sugars such as maltose or sucrose, albumin, salts,etc. Other adjuvants are described for example in Remington'sPharmaceutical Sciences by E. W. Martin. Such compositions will containan effective amount of the conjugate hereof together with a suitableamount of vehicle in order to prepare pharmaceutically acceptablecompositions suitable for effective administration to the host. Forexample, the conjugate may be parenterally administered to subjectssuffering from hemophilia A at a dosage that may vary with the severityof the bleeding episode. The average doses administered intraveneouslyare in the range of 40 units per kilogram for pre-operative indications,15 to 20 units per kilogram for minor hemorrhaging, and 20 to 40 unitsper kilogram administered over an 8-hours period for a maintenance dose.

In one embodiment the inventive method involves replacing one or moresurface BDD amino acids with a cysteine, producing the cysteine muteinin a mammalian expression system, reducing a cysteine which has beencapped during expression by cysteine from growth media, removing thereductant to allow BDD disulfides to reform, and reacting with acysteine-specific biocompatible polymer reagent, such as such asPEG-maleimide. Examples of such reagents are PEG-maleimide with PEGsizes such as 5, 22, or 43 kD available from Nektar Therapeutics of SanCarlos, Calif. under Nektar catalog numbers 2D2M0H01 mPEG-MAL MW 5,000Da, 2D2M0P01 mPEG-MAL MW 20 kD, 2D3X0P01 mPEG2-MAL MW 40 kD,respectively, or 12 or 33 kD available from NOF Corporation, Tokyo,Japan under NOF catalog number Sunbright ME-120MA and SunbrightME-300MA, respectively. The PEGylated product is purified usingion-exchange chromatography to remove unreacted PEG and usingsize-exclusion chromatography to remove unreacted BDD. This method canbe used to identify and selectively shield any unfavorable interactionswith FVIII such as receptor-mediated clearance, inhibitory antibodybinding, and degradation by proteolytic enzymes. We noted that the PEGreagent supplied by Nektar or NOF as 5 kD tested as 6 kD in ourlaboratory, and similarly the PEG reagent supplied as linear 20 kDtested as 22 kD, that supplied as 40 kD tested as 43 kD and thatsupplied as 60 kD tested as 64 kD in our laboratory. To avoid confusion,we use the molecular weight as tested in our laboratory in thediscussion herein, except for the 5 kD PEG, which we report as 5 kD asthe manufacturer identified it.

In addition to cysteine mutations at positions 491 and 1808 of BDD(disclosed above), positions 487, 496, 504, 468, 1810, 1812, 1813, 1815,1795, 1796, 1803, and 1804 were mutated to cysteine to potentially allowblockage of LRP binding upon PEGylation. Also, positions 377, 378, and556 were mutated to cysteine to allow blockage of both LRP and HSPGbinding upon PEGylation. Positions 81, 129, 422, 523, 570, 1864, 1911,2091, and 2284 were selected to be equally spaced on BDD so thatsite-directed PEGylation with large PEGs (>40 kD) at these positionstogether with PEGylation at the native glycosylation sites (41, 239, and2118) and LRP binding sites should completely cover the surface of BDDand identify novel clearance mechanism for BDD.

In one embodiment, the cell culture medium contains cysteines that “cap”the cysteine residues on the mutein by forming disulfide bonds. In thepreparation of the conjugate, the cysteine mutein produced in therecombinant system is capped with a cysteine from the medium and thiscap is removed by mild reduction that releases the cap before adding thecysteine-specific polymer reagent. Other methods known in the art forsite-specific mutation of FVIII may also be used, as would be apparentto one of skill in the art.

EXAMPLES

STRUCTURE ACTIVITY RELATIONSHIP ANALYSIS OF FVIII. FVIII and BDD FVIIIare very large complex molecules with many different sites involved inbiological reactions. Previous attempts to covalently modify them toimprove pharmacokinetic properties had mixed results. That the moleculescould be specifically mutated and then a polymer added in asite-specific manner was surprising. Furthermore, the results ofimproved pharmacokinetic properties and retained activity weresurprising also, given the problems with past polymeric conjugatescausing nonspecific addition and reduced activity.

In one embodiment, the invention concerns site-directed mutagenesisusing cysteine-specific ligands such as PEG-maleimide. A non-mutated BDDdoes not have any available cysteines to react with a PEG-maleimide, soonly the mutated cysteine position will be the site of PEGylation. Morespecifically, BDD FVIII has 19 cysteines, 16 of which form disulfidesand the other 3 of which are free cysteines (McMullen et al., 1995,Protein Sci. 4, pp. 740-746). The structural model of BDD suggests thatall 3 free cysteines are buried (Stoliova-McPhie et al., 2002, Blood 99,pp. 1215-1223). Because oxidized cysteines cannot be PEGylated byPEG-maleimides, the 16 cysteines that form disulfides in BDD cannot bePEGylated without being first reduced. Based on the structural models ofBDD, the 3 free cysteines in BDD may not be PEGylated without firstdenaturing the protein to expose these cysteines to the PEG reagent.Thus, it does not appear feasible to achieve specific PEGylation of BDDby PEGylation at native cysteine residues without dramatically alteringthe BDD structure, which will most likely destroy its function.

The redox state of the 4 cysteines in the B domain of full-length FVIIIis unknown. PEGylation of the 4 cysteines in the B domain may bepossible if they do not form disulfides and are surface exposed.However, because full-length FVIII and BDD have a similarpharmacokinetic (PK) profile and similar half-lives in vivo (Gruppo etal., 2003, Haemophilia 9, pp. 251-260), B domain PEGylation is unlikelyto result in improved plasma half-life unless the PEG happens to alsoprotect non-B domain regions.

To determine the predefined site on a polypeptide having FVIII activityfor polymer attachment that will retain factor VIII activity and improvepharmacokinetics, the following guidelines are presented based on BDDFVIII. Modifications should be targeted toward clearance, inactivation,and immunogenic mechanisms such as LRP, HSPG, APC, and inhibitoryantibody binding sites. Stoilova-McPhie, S. et al., 2002, Blood 99(4),pp. 1215-23 shows the structure of BDD. For example, to prolonghalf-life, a single PEG can be introduced at a specific site at or nearLRP binding sites in A2 residues 484-509 and A3 residues 1811-1818.Introduction of the bulky PEG at these sites should disrupt FVIII'sability to bind LRP and reduce the clearance of FVIII from circulation.It is also believed that to prolong half-life without significantlyaffecting activity that a PEG can be introduced at residue 1648, whichis at the junction of the B domain and the A3 domain in the full-lengthmolecule and in the 14-amino acid linker I the BDD between the A2 and A3domains.

Specificity of PEGylation can be achieved by engineering single cysteineresidues into the A2 or A3 domains using recombinant DNA mutagenesistechniques followed by site-specific PEGylation of the introducedcysteine with a cysteine-specific PEG reagent such as PEG-maleimide.Another advantage of PEGylating at 484-509 and 1811-1818 is that thesetwo epitopes represent two of the three major classes of inhibitoryantigenic sites in patients. To achieve maximal effect of improvedcirculating half-life and reduction of immunogenic response, both A2 andA3 LRP binding sites can be PEGylated to yield a diPEGylated product. Itshould be noted that PEGylation within the 1811-1818 region may lead tosignificant loss of activity since this region is also involved in FIXbinding. Site-directed PEGylation within 558-565 should abolish HSPGbinding, but may also reduce activity as this region also binds to FIX.

Additional surface sites can be PEGylated to identify novel clearancemechanism of FVIII. PEGylation of the A2 domain may offer additionaladvantage in that the A2 domain dissociates from FVIII upon activationand is presumably removed from circulation faster than the rest of FVIIImolecule because of its smaller size. PEGylated A2, on the other hand,may be big enough to escape kidney clearance and have a comparableplasma half-life to the rest of FVIII and thus can reconstitute theactivated FVIII in vivo.

IDENTIFICATION OF PEGylation SITES IN A2 AND A3 REGIONS. Five positions(Y487, L491, K496, L504 and Q468 corresponding to PEG1-5 positions) ator near the putative A2 LRP binding region were selected as examples forsite-directed PEGylation based on the high surface exposure and outwarddirection of their Ca to C13 trajectory. Furthermore, these residues areroughly equidistant from each other in the three-dimensional structureof the molecule, so that together they can represent this entire region.Eight positions (1808, 1810, 1812, 1813, 1815, 1795, 1796, 1803, 1804corresponding to PEG6-14) at or near the putative A3 LRP binding regionwere selected as examples for site-directed PEGylation. PEG6 (K1808) isadjacent to 1811-1818 and the natural N-linked glycosylation site at1810. PEGylation at position 1810 (PEG7) will replace the sugar with aPEG. Mutation at the PEG8 position T1812 will also abolish theglycosylation site. Although the PEG9 position (K1813) was predicted tobe pointing inward, it was selected in case the structure model is notcorrect. PEG10 (Y1815) is a bulky hydrophobic amino acid within the LRPbinding loop, and may be a critical interacting residue sincehydrophobic amino acids are typically found at the center ofprotein-protein interactions. Because the 1811-1818 region has beenreported to be involved in both LRP and FIX binding, PEGylation withinthis loop was thought possibly to result in reduced activity. Thus,PEG11-PEG14 (1795, 1796, 1803, 1804) were designed to be near the1811-1818 loop but not within the loop so that one can dissociate LRPand FIX binding with different PEG sizes.

To block both LRP binding sites simultaneously, double PEGylation at,for example, the PEG2 and PEG6 position, can be generated.

Since the 558-565 region has been shown to bind to both HSPG and FIX, nosites were designed within this region. Instead, PEG15-PEG17 (377, 378,and 556) were designed in between the A2 LRP and HSPG binding regions sothat an attached PEG may interfere both interactions and disruptpossible interactions between them. Additional sites that are surfaceexposed and outwardly pointing could also be selected within or near theLRP and HPSG binding regions. To identify novel clearance mechanisms,FVIII can be systematically PEGylated. In addition to PEG1-17, the threeother natural glycosylation sites, namely, N41, N239, and N2118corresponding to PEG18-20 can be used as tethering points for PEGylationsince they should be surface exposed. Surface areas within a 20 angstromradius from the C13 atoms of PEG2, PEG6, and the four glycosylationsites were mapped onto the BDD model in addition to functionalinteraction sites for vWF, FIX, FX, phospholipid, and thrombin.

PEG21-29 corresponding to Y81, F129, K422, K523, K570, N1864, T1911,Q2091, and Q2284 were then selected based on their ability to covernearly the entire remaining BDD surface with a 20 angstrom radius fromeach of their C13 atoms. These positions were also selected because theyare fully exposed, outwardly pointing, and far away from naturalcysteines to minimize possible incorrect disulfide formation. The 20angstrom radius is chosen because a large PEG, such as a 64 kD branchedPEG, is expected to have the potential to cover a sphere with about a 20angstrom radius. PEGylation of PEG21-29 together with PEG2 and PEG6 andglycosylation sites PEG18, 19, and 20 is likely to protect nearly theentire non-functional surface of FVIII.

PEGylation positions that lead to enhanced properties such as improvedPK profile, greater stability, or reduced immunogenicity can be combinedto generate multi-PEGylated product with maximally enhanced properties.PEG30 and PEG31 were designed by removing the exposed disulfides in A2and A3 domain, respectively. PEG30, or C630A, should free up itsdisulfide partner C711 for PEGylation. Likewise, PEG31, C1899A shouldallow C1903 to be PEGylated.

MUTAGENESIS. Substrates for site-directed PEGylation of FVIII may begenerated by introducing a cysteine codon at the site chosen forPEGylation. The Stratagene cQuickChange™ II site-directed mutagenesiskit was used to make all of the PEG mutants (Stratagene kit 200523 fromStratagene Corporation, La Jolla, Calif.). The cQuikChange™site-directed mutagenesis method is performed using PfuTurbo® DNApolymerase and a temperature cycler. Two complimentary oligonucleotideprimers, containing the desired mutation, are elongated using PfuTurbo,which will not displace the primers. dsDNA containing the wildtype FVIIIgene is used as a template. Following multiple elongation cycles, theproduct is digested with DpnI endonuclease, which is specific formethylated DNA. The newly synthesized DNA, containing the mutation, isnot methylated, whereas the parental wild-type DNA is methylated. Thedigested DNA is then used to transform XL-1 Blue super-competent cells.

The mutagenesis efficiency is almost 80%. The mutagenesis reactions wereperformed in either pSK207+BDD C2.6 or pSK207+BDD (FIG. 1). Successfulmutagenesis was confirmed by DNA sequencing and appropriate fragments,containing the mutation, were transferred into the FVIII backbone in themammalian expression vector pSS207+BDD. After transfer, all of themutations were again sequence-confirmed. For A3 muteins PEG 6, 7, 8, 9,and 10, mutagenesis was done in the vector pSK207+BDD C2.6. After beingconfirmed by sequencing, the mutant fragment, KpnI/Pme was subclonedinto pSK207+BDD. The BDD mutein was then subcloned into the pSS207+BDDexpression vector. For A3 muteins PEG 11, 12, 13, 14, the mutagenesiswas done directly in the vector pSK207+BDD and sequence-confirmed mutantBDD were then subcloned into pSS207+BDD. For A2 muteins PEG 1, 2, 3, 4,5, the mutagenesis was done in the pSK207+BDD C2.6vector. The sequenceconfirmed mutant was subcloned into pSK207+BDD and then to pSS207+BDD.

The Primers (Sense Stand Only) Used for Mutagenesis are Listed for EachReaction

PEG1, Y487C: (SEQ ID NO: 5) GATGTCCGTCCTTTGTGCTCAAGGAGATTACCA PEG2,L491C: (SEQ ID NO: 6) TTGTATTCAAGGAGATGCCCAAAAGGTGTAAAAC PEG3, K496C:(SEQ ID NO: 7) TTACCAAAAGGTGTATGCCATTTGAAGGATTTTC PEG4, L504C: (SEQ IDNO: 8) AAGGATTTTCCAATTTGCCCAGGAGAAATATTC PEG5, Q468C: (SEQ ID NO: 9)GATTATATTTAAGAATTGCGCAAGCAGACCATAT PEG6, K1808C: (SEQ ID NO: 10)TAGAAAAAACTTTGTCTGCCCTAATGAAACCAAAAC PEG7, N1810C: (SEQ ID NO: 11)AACTTTGTCAAGCCTTGCGAAACCAAAACTTAC PEG8, T1812C: (SEQ ID NO: 12)GTCAAGCCTAATGAATGCAAAACTTACTTTTGGA PEG9, K1813C: (SEQ ID NO: 13)CAAGCCTAATGAAACCTGCACTTACTTTTGGAAAG PEG10, Y1815C: (SEQ ID NO: 14)CTAATGAAACCAAAACTTGCTTTTGGAAAGTGCAAC PEG11, D1795C: (SEQ ID NO: 15)ATTTCTTATGAGGAATGCCAGAGGCAAGGAGCA PEG12, Q1796C: (SEQ ID NO: 16)TCTTATGAGGAAGATTGCAGGCAAGGAGCAGAA PEG13, R1803C: (SEQ ID NO: 17)CAAGGAGCAGAACCTTGCAAAAACTTTGTCAAGCCT PEG14, K1804C: (SEQ ID NO: 18)GGAGCAGAACCTAGATGCAACTTTGTCAAGCCT PEG15, K377C: (SEQ ID NO: 19)CGCTCAGTTGCCAAGTGTCATCCTAAAACTTGG PEG16, H378C: (SEQ ID NO: 20)TCAGTTGCCAAGAAGTGTCCTAAAACTTGGGTA PEG17, K556C: (SEQ ID NO: 21)CTCCTCATCTGCTACTGCGAATCTGTAGATCAA PEG18, N41C: (SEQ ID NO: 22)CAAAATCTTTTCCATTCTGCACCTCAGTCGTGTAC PEG19, N239C: (SEQ ID NO: 23)GTCAATGGTTATGTATGCAGGTCTCTGCCAGGT PEG20, N2118C: (SEQ ID NO: 24)CAGACTTATCGAGGATGTTCCACTGGAACCTTA PEG21, Y81C: (SEQ ID NO: 25)ATCCAGGCTGAGGTTTGTGATACAGTGGTCATT PEG22, F129C: (SEQ ID NO: 26)GAAGATGATAAAGTCTGTCCTGGTGGAAGCCAT PEG23, K422C: (SEQ ID NO: 27)CAGCGGATTGGTAGGTGTTACAAAAAAGTCCGA PEG24, K523C: (SEQ ID NO: 28)GAAGATGGGCCAACTTGCTCAGATCCTCGGTGC PEG25, K570C: (SEQ ID NO: 29)CAGATAATGTCAGACTGCAGGAATGTCATCCTG PEG26, N1864C: (SEQ ID NO: 30)CACACTAACACACTGTGTCCTGCTCATGGGAGA PEG27, T1911C, (SEQ ID NO: 31)CAGATGGAAGATCCCTGCTTTAAAGAGAATTAT PEG28, Q2091C: (SEQ ID NO: 32)ACCCAGGGTGCCCGTTGCAAGTTCTCCAGCCTC PEG29, Q2284C: (SEQ ID NO: 33)AAAGTAAAGGTTTTTTGCGGAAATCAAGACTCC PEG30, C630A: (SEQ ID NO: 34)TTGCAGTTGTCAGTTGCTTTGCATGAGGTGGCA PEG31, C1899A: (SEQ ID NO: 35)AATATGGAAAGAAACGCTAGGGCTCCCTGCAAT

MUTEIN EXPRESSION. After insertion in a vector that confers resistanceto Hygromycin B, the PEG muteins were transfected into HKB11 cells (U.S.Pat. No. 6,136,599) complexed with 293 Fectin Transfection Reagent(Invitrogen Corp. Cat#12347-019) per the manufacturer's instructions.FVIII expression at three days post-transfection was assessed by Coatestchromogenic assay (Chromogenix Corp. Cat#821033, see Example 12Chromogenic Assay) (Table 1). The transfected cells were then placedunder selective pressure with 50 μg/ml of Hyg B in a growth mediumsupplemented with 5% FBS. When Hyg B-resistant colonies appeared, theywere manually picked and screened for FVIII expression by Coatestchromogenic assay. The FVIII expressing stable cells were then adaptedto a medium containing HPPS supplement. The cells were expanded andseeded at 1×106 cells/ml in shaking flasks with fresh media. Tissueculture fluid (TCF), harvested after 3 days, was used for purificationof FVIII BDD muteins. The FVIII activity of the TCF was assayed byCoatest (Table 1).

TABLE 1 Expression level of PEG Muteins from transient and stabletransfections. Summary of PEG Mutein Titers Titer (IU/ml) MutationMutein ID Transient Stable Cells Y487C PEG1 0.07 N/A L491C PEG2 0.601.96 K496C PEG3 0.45 N/A L504C PEG4 0.38 5.57 Q468C PEG5 0.69 8.14K1808C PEG6 0.54 2.73 N1810C PEG7 0.21 0.5  T1812C PEG8 0.16 N/A K1813CPEG9 0.35 7.74 Y1815C PEG10 0.09 N/A D1795C PEG11 0.27 N/A Q1796C PEG120.29 N/A R1803C PEG13 0.11 N/A K1804C PEG14 0.18 1.14 L491C/K1808CPEG2+6 0.11 2.48 L491C/K1804C PEG2+14 0.13 7.19 K377C PEG15 0.11 12.58 H378C PEG16 0.15 0.97 K556C PEG17 0.09 0.15 N41C PEG18 0.05 N/A N239CPEG19 0.16 N/A N2118C PEG20 0.13 N/A Y81C PEG21 0.36 N/A F129C PEG220.25 2.55 K422C PEG23 0.28 N/A K523C PEG24 <0.05 N/A K570C PEG25 <0.05N/A N1864C PEG26 0.15 N/A T1911C PEG27 0.28 N/A Q2091C PEG28 0.20 N/AQ2284C PEG29 0.17 N/A C630A PEG30 <0.05 0.20 C1899A PEG31 0.30 1.80

MUTEIN PURIFICATION. Upon collecting the cell culture supernatantcontaining the secreted mutein FVIII protein, the supernatant isfiltered through a 0.2 micron membrane filter to remove any remainingcells. The supernatant is then concentrated by either ultrafiltration oranion exchange. It is then applied to an immunoaffinity column where thecell culture media components and the majority of the host cell proteinimpurities are removed. The immunoaffinity column eluate is then bufferexchanged by diafiltration into a formulation buffer containing sucroseand frozen. Yield and recovery of protein across a monoclonal FVIIIantibody column was assessed by chromogenic assay. Samples of load, flowthrough, various eluate fractions, strip, and the diafiltered eluate ofa chromatography run were assayed for FVIII activity (Table 2). Table 2shows the recovery of the PEG2 mutein from a monoclonal antibody column.The antibodies are C7F7 antibodies. The percent recovery in Table 2 isdetermined by the chromogenic assay. The final yield was 73%. Shown inFIG. 2 is a plot of the UV absorbance at 280 nm with respect to time forthe PEG2 protein purified over a monoclonal FVIII antibodychromatography column. The chromatography was performed using an AKTA®Explorer 100 chromatography system from Amersham Bioscience. Thisinstrument employs a multi-wavelength UV-Visible monitor and a 2 mm flowcell. The PEG2 mutein is eluted from the column in the presence of highsalt and elution peak is indicated by both the absorbance at 280 nm andFVIII activity assay.

TABLE 2 Recovery of PEG2 mutein from monoclonal FVIII antibody column.Step % Recovery C7F7 Load 100 C7F7 Flow through 1.1 C7F7 Wash 0.2 C7F7Eluate 86 C7F7 Strip 0.0 Post UF/DF 73

PEGYLATION. Native full-length FVIII or BDD cannot be PEGylated bycysteine-specific PEGs without reduction and denaturation at over100-fold excess PEG: protein ratio (data not shown), confirming thehypothesis based on the BDD structure model that all native cysteinesform disulfides or are buried within FVIII. FVIII cysteine muteinsexpressed and purified using the standard protocols listed above couldnot be PEGylated with a cysteine-specific PEG maleimide reagent,presumably because the introduced FVIII cysteine is “capped” by reactingwith sulfhydryl groups such as cysteine and β-mecaptoethanol present inthe cell growth media. This issue can potentially be resolved byeliminating cysteines and β-mecaptoethanol from the culture media, butthis may lead to lower FVIII production and would not preventsulfhydryls released by the cells from blocking the introduced FVIIIcysteine.

In another aspect of the invention, a three-step method was developed toallow site-specific PEGylation of FVIII (FIG. 3). In step 1, thepurified FVIII cysteine mutein at about 1 μM is mildly reduced withreductants such as about 0.7 mM Tris(2-carboxyethyl)phosphine (TCEP) or0.07 mM dithiothreitol (DTT) for 30 minutes at 4° C. to release the“cap.” In step 2, the reductant is removed along with the “cap” by asize-exclusion chromatography (SEC) method such as running the samplethrough a spin column (BioRad®) to allow FVIII disulfides to reformwhile leaving the introduced cysteine free and reduced. In step 3, atleast 30 minutes after the removal of the reductant, the freed FVIIIcysteine mutein is treated with at least 10-fold molar excess ofPEG-maleimide with sizes ranging from 5 to 64 kD (Nektar Therapeuticsand N.O.F. Corporation) for at least 1 hour at 4° C. This method yieldshighly consistent product profile with reproducible data for dozens ofreactions repeated by different individuals.

Because the spin column method for removal of TCEP is not scaleable, gelfiltration desalting chromatography was selected. However, upon testingthis method using a TCEP spike sample, it was shown that the TCEP elutedat measurable levels in the column void and not just in the saltfraction as would be expected from a molecule with its low molecularweight. Western Blot assays showed significant background PEGylationprobably due to incomplete removal of TCEP. In the meantime separateexperiments showed that C7F7 purified material could be significantlypurified further from other protein impurities using an anion exchangechromatography media combined with a salt gradient. It was then decidedto reduce the C7F7 material with TCEP as described above and thenprocess the material over the anion exchange column. Because of chargedifference the FVIII protein would be retained while the TCEP would flowthrough the column and not be retained. At the same time during thegradient salt elution the FVIII protein would be purified away from themajority of remaining protein impurities. This meant that the lateroccurring PEGylation would be theoretically more homogeneous with purerstarting material. However, upon testing with a spike sample of TCEP, itwas shown that measurable levels of TCEP were found eluting in thegradient with the FVIII. Therefore it was decided to implement gelfiltration desalting chromatography after anion exchange chromatographyso these two steps when used in sequence would result in completeremoval of TCEP and elimination of non-specific PEGylation.

PEGYLATION ANALYSIS BY SDS PAGE AND WESTERN BLOT. The PEGylated productcan be analyzed by electrophoresis on a reducing 6% TrisGlycine SDSpolyacrylamide gel (Invitrogen). Following electrophoresis, the gel canbe stained with Coomassie Blue to identify all the proteins or subjectedto a standard Western Blot protocol to identify PEGylation pattern ondifferent regions of FVIII. Staining of the blot with a mouse monoclonalR8B12 or C7F7 antibody raised against the C-terminal region of the FVIIIheavy chain or the N-terminal region of the VIII light chain,respectively, should identify PEGylation of the respective chains.Staining with the 413 antibody against the 484-509 region of FVIII willdetermine whether PEGylation is indeed site-specific or not for muteinssuch as PEG1-4. Likewise, staining with the CLB-CAg A antibody thatrecognizes the 1801-1823 region of FVIII will determine if PEGylation issite-specific or not for muteins such as PEG6-10.

PEG2 (L491C) PEGylation was shown to be selective for the heavy chainover light chain and particularly selective for the 484-509 region (FIG.4) while PEG6 (K1808C) was shown to be selective for the light chainover the heavy chain (FIG. 5).

For the study depicted in FIG. 4, the PEG2 mutein (lanes 1 and 8) isreduced with TCEP followed by TCEP removal (lanes 2 and 9) and treatmentwith 5, 12, 22, 33, or 43 kD PEG-maleimide (lanes 3-7 and 10-14).UnPEGylated FVIII runs as unprocessed (H+L) and processed heavy (H) andlight (L) chain bands. All three bands are detectable on the CoomassieBlue stained gel (lower right) whereas Western Staining withchain-specific antibodies reveal only the unprocessed and thecorresponding chain. Using R8B12 staining (upper left), the heavy chain(H) band is dramatically reduced in intensity when PEG2 is treated withPEG-maleimide and a new band is created that runs higher than the parentH band proportional to the size of the PEG. Using C7F7 staining (lowerleft), the light chain (L) bands (multiple bands due to heterogenousglycosylation) do not change intensity. The unprocessed H+L band forboth stains are shifted because the H chain is part of the unprocessedFVIII. Coomassie staining also confirms much more PEGylation of theheavy chain, i.e. reduction of H band intensity, than of the lightchain. Finally, the PEGylated bands lose relatively more intensity onthe 413 antibody stain (upper right) than R8B12 stain in a PEGsize-dependent fashion presumably due to site-specific PEGylation of491, which blocks the binding of 413 antibody to 484-509. Quantities ofFVIII loaded per lane are about 30 ng for the two left gels, about 1000ng for the upper right gel, and about 2000 ng for the lower right gel.

Reduction followed by removal of reductant does not change the migrationof FVIII (lane 1 vs. 2 and 8 vs. 9). Addition of 22 kD PEG to PEG2blocks the binding of the 413 antibody, consistent with specificPEGylation at the 491 position (FIG. 4 upper right gel). This alsosuggests that PEGylated PEG2 will have lower immunogenicity in manbecause the 413 antibody has been shown to share the same epitope ashuman A2 inhibitory antibodies (Scandella et al., 1992, Thromb. Haemost.67, pp. 665-71).

For the study depicted in FIG. 5, the PEG6 mutein is reduced with TCEPfollowed by TCEP removal (lanes 1 and 6) and treatment with 5, 12, 22,or 33 kD PEG-maleimide (lanes 2-5 and 7-10). UnPEGylated FVIII runs asunprocessed (H+L) and processed heavy (H) and light (L) chain bands.Because the PEG6 (K1808) mutation resides on the light chain, PEGylationwas detected only on the light chain and not the heavy chain. Amount ofFVIII loaded per lane is about 100 ng for the left gel and about 30 ngfor the right gel.

The BDD that was run as a control did not show any significantPEGylation upon treatment with greater than 100-fold molar excess ofPEG-maleimide even after the reduction and reductant removal proceduredescribed above (FIG. 6A-6D). The same method was also applied to PEG4and PEGS (FIG. 6A-6D). Compared to PEG2, these muteins were notPEGylated as efficiently, but they were selective for the heavy chainsimilar to PEG2 (L491C). PEG6 (K1808C) PEGylation efficiency isrelatively low, perhaps because it is very close to the N-linkedglycosylation site at N1810, which may block PEGylation at position1808. Thus, we designed PEG7 (N1810C) to remove the native glycosylationsite at 1810. PEG7 shows improved PEGylation efficiency compared to PEG6in a head-to-head comparison (FIG. 6E). Similarly PEG15 shows slightlybetter PEGylation efficiency than PEG2. PEG2+6, a double mutant of BDD,can be PEGylated on both heavy and light chains since PEG2 is a heavychain cysteine mutation while PEG6 is a light chain mutation (FIG. 6F).This method was also applied to wildtype full-length FVIII (FIG. 6G).PEGylation was detected for the largest fragment of heavy chain thatincludes A1, A2, and most of the B domain. The PEGylation patternsuggests monoPEGylation and that there is only a single cysteinePEGylated.

PEGYLATION ANALYSIS BY THROMBIN CLEAVAGE AND WESTERN BLOT. The PEGylatedproduct can be treated with thrombin (40 IU/ug FVIII) at 37° C. for 30minutes. The thrombin used also contains APC as a contaminant. Thrombincleavage will generate the 50 kD A1 and 43 kD A2 domains from the heavychain while the APC cleavage will split the A2 domain further into the21 and 22 kD fragments (FIG. 7). Staining with the R8B12 antibody, whichrecognizes the C-terminus of the heavy chain, will identify only theintact A2 domain and the 21 kD C-terminal fragment (FVIII 562-740).Thus, if PEG2 PEGylation was specific for position 491, the 43 kD A2domain should be PEGylated but not the 21 kD C-terminal fragment. Thiswas indeed confirmed by the Western blot for the 22 kD PEGylated PEG2shown on FIG. 7. Thus, by elimination, PEG2 PEGylation has beenlocalized to the N-terminal 22 kD fragment (FVIII 373-561) of A2 domain.Since PEG-maleimide is completely selective for cysteines at pH 6.8 andthe only native FVIII cysteines within 373-561 come from a burieddisulfide between 528 and 554, PEG2 is very likely PEGylated on theintroduced cysteine at position 491. Western staining ofthrombin-treated PEGylated PEG2 with a FVIII heavy chain N-terminalantibody showed no PEGylation of the A1 domain (data not shown).Selective PEGylation of PEG2 using thrombin cleavage method has alsobeen confirmed for PEGs of 5, 12, 33, and 43 kDs (data not shown).Thrombin cleavage of PEGylated wildtype full-length FVIII shows thatonly B domain is PEGylated (FIG. 8)

PEGYLATION ANALYSIS BY IODINE STAINING. To confirm that the newlycreated bands on Coomassie Blue and Western staining were indeedPEGylated bands, barium-iodine staining, which is specific for PEG, wasused (FIG. 9). PEGylated PEG2 was run on a 6% TrisGlycine gel(Invitrogen) and stained with the R8B12 heavy chain antibody or abarium-iodine solution (Lee et al, Pharm Dev Technol. 1999 4:269-275).The PEGylated bands matched between the two stains using the molecularweight marker to line them up, thus confirming FVIII heavy chainPEGylation.

PEGYLATION ANALYSIS BY MALDI-MASS SPEC. To confirm the PEGylation of theA2 domain in the heavy chain, the rFVIII sample, before and afterPEGylation was analyzed by matrix-assisted laser desorption/ionization(MALDI) mass spectrometry. The samples were mixed and crystallized onthe MALDI target plate with a sinapinic acid matrix in 30% acetonitrile,0.1% TFA. They were then analyzed in a Voyager DE-PRO spectrometer inpositive, linear mode. The results, shown in FIG. 10, showed the lightchain of PEG2 centered at 83 kD and the heavy chain (HC) at 89 kD. Thespectrum acquired for the PEGylated sample showed a drop in the HC peakand a new peak, centered at 111 kD, to form. This confirms PEGylation ofthe heavy chain. No PEGylated light chain (at 105 kD) was observed abovedetection limit.

The samples were then both subjected to thrombin digestion at 20 unitsof thrombin/mg FVIII at 37° C. for 30 minutes, following FVIIIconcentration determination by amino acid analysis (CommonwealthBiotechnologies, Inc). The heavy chain was cleaved into a 46 kD (A1)N-terminal fraction and a 43 kD (A2) fraction. The MALDI spectrumacquired for the PEGylated sample (FIG. 11) shows the loss of the 43 kDpeak and the development of a new 65 kD peak, due to the PEGylated A2domain. PEGylation of the LC is again not observed above the detectionlimit. These results again confirm PEGylation of the A2 domain of FVIII.The same analysis was applied to PEGylated PEG6, confirming PEGylationof the light chain A3C1C2 fragment (FIG. 12).

Activity Measurement

COAGULATION ASSAY. The clotting FVIII:C test method is a one-stage assaybased upon the activated partial thromboplastin time (aPTT). FVIII actsas a cofactor in the presence of Factor IXa, calcium, and phospholipidin the enzymatic conversion of Factor X to Xa. In this assay, thediluted test samples are incubated at 37° C. with a mixture of FVIIIdeficient plasma substrate and aPTT reagent. Calcium chloride is addedto the incubated mixture and clotting is initiated. An inverserelationship exists between the time (seconds) it takes for a clot toform and logarithm of the concentration of FVIII:C. Activity levels forunknown samples are interpolated by comparing the clotting times ofvarious dilutions of test material with a curve constructed from aseries of dilutions of standard material of known activity and arereported in International Units per mL (IU/mL).

CHROMOGENIC ASSAY. The chromogenic assay method consists of twoconsecutive steps where the intensity of color is proportional to theFVIII activity. In the first step, Factor X is activated to FXa by FIXawith its cofactor, FVIIIa, in the presence of optimal amounts of calciumions and phospholipids. Excess amounts of Factor X are present such thatthe rate of activation of Factor X is solely dependent on the amount ofFVIII. In the second step, Factor Xa hydrolyzes the chromogenicsubstrate to yield a chromophore and the color intensity is readphotometrically at 405 nm. Potency of an unknown is calculated and thevalidity of the assay is checked with the slope-ratio statisticalmethod. Activity is reported in International Units per mL (IU/mL).

The 1811-1818 loop is involved in binding to FIX, but the importance ofindividual positions within this loop has not been determined. PEG7-10muteins display nearly identical specific chromogenic activity relativeto native FVIII (Table 3). Table 3 shows the percent specific activity(S.A.) of PEG muteins and PEGylated PEG2 or PEG6 relative to BDD. S.A.was determined by dividing the chromogenic, coagulation, or vWF bindingactivity by the total antigen ELISA (TAE) value. The S.A. of PEGylatedmuteins was then divided by the S.A. of BDD (8 IU/ug chromogenic, 5IU/ug coagulation, and 1 vWF/TAE) and multiplied by 100 to obtain thepercent S.A. listed in Table 3 under the headings chromogenic,coagulation and vWF/TAE.

TABLE 3 Percent specific activity (S.A.) of PEG muteins and PEGylatedPEG2 and PEG6 relative to BDD. Chromo- Coagu- Mutation genic lationvWF/TAE BDD 100 100 100 PEG1 Y487C PEG2 L491C 125 130 138 PEG2 red L491C137 141 98 PEG2-5 kD PEG L491C 124 93 125 PEG2-12 kD PEG L491C 118 25 71PEG2-22 kD PEG L491C 103 13 87 PEG2-33 kD PEG L491C 130 17 59 PEG2-43 kDPEG L491C 91 9 57 PEG3 K496C PEG4 L504C PEG5 Q468C 92 PEG6 K1808C 83 60100 PEG6-33 kD PEG K1808C 42 6 90 PEG7 N1810C 100 PEG8 T1812C 100 PEG9K1813C 83 PEG10 Y1815C 75 PEG11 D1795C PEG12 Q1796C PEG13 R1803C PEG14K1804C PEG2+6 491C/1808C PEG15 K377C 82 PEG16 H378C 126 PEG17 K556C 43PEG18 N41C 80 PEG19 N239C PEG20 N2118C 127 PEG21 Y81C PEG22 F129C 83PEG23 K422C PEG24 K523C PEG25 K570C PEG26 N1864C PEG27 T1911C PEG28Q2091C PEG29 Q2284C

As used in Table 3, “PEG2 red” is PEG2 mutein that has been treated withreductant followed by the removal of reductant. This reduction proceduredid not significantly alter the three functional activities of FVIII.PEG2 mutein conjugated to PEGs ranging from 5 kD (PEG2-5 kD) to 43 kD(PEG2-43 kD) did not lose a significant amount of chromogenic activity,but had greatly lower coagulation activity as the PEG size increasesbeyond 5 kD. There may be a modest reduction in vWF binding for largersize PEGylated PEG2 also.

TOTAL ANTIGEN ELISA (TAE). FVIII is captured on a microtiter plate thathas been coated with a polyclonal FVIII antibody. The FVIII bound isdetected with a biotinylated polyclonal rFVIII antibody and streptavidinhorseradish peroxidase (HRP) conjugate. The peroxidase-streptavidincomplex produces a color reaction upon addition of thetetramethylbenzidine (TMB) substrate. Sample concentrations areinterpolated from a standard curve using four parameter fit models.FVIII results are reported in μg/m L.

vWF BINDING ELISA. FVIII is allowed to bind to vWf in Severe HemophilicPlasma in solution. The FVIII-vWf complex is then captured on amicrotiter plate that has been coated with a vWf-specific monoclonalantibody. The FVIII bound to the vWf is detected with a FVIII polyclonalantibody and a horseradish peroxidase-anti-rabbit conjugate. Theperoxidase-conjugated antibody complex produces a color reaction uponaddition of the substrate. Sample concentrations are interpolated from astandard curve using four parameter fit model. FVIII binding results arereported in μg/m L. There was no significant impact on any of theactivities upon PEGylation, which would be consistent with PEGylation atthe B domain.

TABLE 4 Specific activity (S.A.) of wildtype full length FVIII (KG-2)before and after PEGylation with different sizes of PEG. TAE CoagulationAssay Chromogenic Assay vWF ELISA Sample ug/mL IU/mL IU/ug % Start IU/mLIU/ug % Start ug/mL vWF/TAE % Start KG-2 start 1.31 4.8 3.6 100 5.60 4.3100 0.42 0.32 100 Reduced only 0.93 3.1 3.4 93 4.08 4.4 103 KG-2-5kD PEG0.71 2.5 3.5 96 3.09 4.3 102 KG-2-12kD PEG 0.59 2.3 3.9 107 2.99 5.0 118KG-2-22kD PEG 0.63 2.5 3.9 108 3.06 4.8 113 0.19 0.30 94 KG-2-30kD PEG0.59 2.5 4.1 114 3.01 5.1 119 0.19 0.32 100 KG-2-43kD PEG 0.52 2.4 4.6128 2.86 5.5 129

PURIFICATION OF PEGylated FVIII BY ION-EXCHANGE CHROMATOGRAPHY.PEGylated FVIII is applied to an anion exchange column or cationexchange column where the protein binds to the column while any excessfree PEG reagent does not bind and is removed in the flow through. ThePEG mutein is then eluted from the column with a sodium chloridegradient. A barium-iodine stained 4-12% Bis-Tris gel of load, flowthrough, and gradient fractions was used to confirm that the columnelution fractions have PEGylated mutein.

PURIFICATION OF PEGylated FVIII BY SIZE-EXCLUSION CHROMATOGRAPHY. Theanion exchange fractions containing the majority of PEG2 mutein arepooled and concentrated by ultrafiltration then applied to a sizeexclusion column. The column is then eluted using the formulationbuffer. Because of the difference in the size and shape of the proteindepends on whether PEG is bound to the protein, this column separatesthe PEGylated PEG2 mutein from that of any remaining PEG2, which is notPEGylated. The PEGylated mutein FVIII fractions are pooled based onhaving the most FVIII activity then frozen for subsequent animal studiesand molecular characterization. FIG. 13 compares the elution ofnon-PEGylated PEG2 mutein versus that of the 43 kD PEGylated PEG2mutein. The PEGylated PEG2 elutes significantly earlier, which indicatesan increase in its size and shape from the covalently attached PEG.

With muteins such as PEG6 that show lower efficiencies of PEGylation,i.e. less than 50%, the most effective purification scheme to yieldhighly pure mono-PEGylated product is to use a combination of cationexchange chromatography followed by size exclusion chromatography. Forexample, with PEG6, the cation exchange chromatography purifies thePEGylated PEG6 (earlier eluting fraction, FIG. 14) away from themajority of un-PEGylated PEG6 (later eluting fraction, FIG. 15). Thesize exclusion chromatography then polishes the PEGylated protein(earlier eluting fraction, FIG. 15) from the remainder of un-PEGylatedprotein (later eluting fraction FIG. 15).

EFFECT OF PEG SIZE ON ACTIVITY. To test whether PEG sizes have an effecton both coagulation and chromogenic activities of FVIII upon PEGylation,purified full-length FVIII, PEG2, PEG6, and PEG14 were reduced by TCEPfollowed by reductant removal and reaction with a buffer control or PEGsranging from 6 kD to 64 kD. The resulting PEGylated FVIII was directlyassayed without removal of excess PEG or unPEGylated FVIII. Controlexperiments showed that the excess PEG has no effect on FVIII activity.

FIG. 16 shows the results of this study. Purified full-length FVIII isrepresented as KG-2 in FIG. 16. The percent activity reported in FIG. 16was determined by dividing the value of sample treated with PEG afterreduction and reductant removal by that of the sample treated withbuffer control taking into consideration the PEGylation yield.PEGylation yields were comparable across all PEGs for any given FVIIIconstruct. They are about 80% for KG-2, PEG2, and PEG14 and about 40%for PEG6. For example, PEG14 buffer control treated has a coagulationactivity of 6.8 IU/mL vs. 3.2 IU/mL for the 12 kD PEGylated PEG14sample. However, the PEGylation efficiency was about 80%, meaning the3.2 IU/mL represents the aggregate activity of about 80% PEGylated andabout 20% unPEGylated. Assuming the unPEGylated sample has the sameactivity as the buffer control treated PEG14, the percent activity ofunPEGylated for the PEGylated PEG14 works out to be 34%=(3.2-6.8 times20%)/(6.8 times 80%).

PEGylation within the A2 or A3 domain at PEG2, PEG6, or PEG14 positionof BDD led to dramatic losses of coagulation activity when PEG sizeincreases beyond 6 kD. However, PEGylation within the B domain at anative B-domain cysteine of the full-length FVIII had no effect on thecoagulation activity. Interestingly, the chromogenic activity is notaffected for all PEGylated constructs. This may be due to assaydifferences. It is possible that the small chromogenic peptide substratehas an easier access to a PEGylated FVIII/FIX/FX complex than the largerprotein substrate used in the coagulation assay. Alternatively, PEG mayaffect activation of the mutein. This would be more readily detected bythe one-stage coagulation assay than the two-stage chromogenic assay.

To confirm the observation of PEG effects on the coagulation activity ofPEG2, 6, and 14, several PEGylated contructs were purified away fromexcess PEG and unPEGylated. Since PEG does not have any effect on thechromogenic activity, the chromogenic to coagulation activity ratio is agood estimate on the relative effect of PEG on coagulation activity(Table 5). Larger PEGs at a given position such as PEG2 and a highernumber of PEGs as in the case with the PEG2+6 construct induce a greaterloss of coagulation activity.

TABLE 5 Ratio of Chromogenic to Coagulation for Purified PEGylated BDD.Chromogenic IU/mL/ Coagulation IU/mL PEGylated BDD Raw Ratio relativeSample ID PEG Ratio to BDD BDD no PEG 1.7 1 PEG2 (pool2) 22 kD 491 9 5PEG2 43 kD* 491 25 15 PEG6 12 kD 1808 5 3 PEG6 (old) 33 kD 1808 13 7PEG6 (new) 33 kD 1808 8 5 PEG2+6 (LSP25) 33 kD at 491, Mono 10 6 PEG2+6(LSP22) 33 kD at 491/1808, Di 24 14 PEG2+6 (ESP) 33 kD at 491/1808/A3,Tri 60 35 PEG22 64 kD* 129 14 8 PEG14 12 kD 1804 3.2 1.9 PEG14 20 kD*1804 4.2 2.5 PEG14 33 kD 1804 5 2.9 PEG2+14 (ESP19) 33 kD at 491/1804,Di 21 12 *branched PEG

RABBIT PK STUDY. To understand the effects of PEGylation on thepharmacokinetics (PK) of FVIII, PK studies were performed in a number ofspecies. NZW SPF rabbits were used for the study: 10 females, 5 rabbitsper group, 2 groups (PEG2 FVIII and 22 kD PEGylated PEG2). Samples werediluted into sterile PBS with a final concentration of 100 IU/mL(chromogenic units). Each rabbit received a dose of 1 ml/kg (100 IU/kg)of the diluted test or control substance via marginal ear vein. Atvarious times post-injection, blood samples (1 mL) were drawn into a 1mL syringe (charged with 100 μL of 3.8% Na-Citrate) from the central earartery at defined time points after dosing. Plasma samples wereincubated with R8B12 heavy chain antibody coated on a 96-well plate tospecifically capture the dosed human FVIII. The activity of the capturedFVIII was determined by the chromogenic assay (FIG. 17). PEGylated PEG2and PEGylated PEG6 were also compared with BDD (FIGS. 18 and 19), withPEGylated muteins showing an improvement in plasma recovery compared toBDD. PEGylated wildtype full-length FVIII did not appear to show muchimprovement (FIG. 20).

MOUSE PK STUDY. As a second species, ICR normal or hemophilic, FVIIIdeficient, mice (Taconic, Hudson, N.Y.) were used in PK studies. Normalmice were used for the study, 5 mice per group per time point. Testmaterials were diluted into formulation buffer to a nominal finalconcentration of 25 IU/mL. Each mouse can be administered 4 mL/kg (˜0.1mL total volume) of the dilute test material via tail vein. Bloodsamples (0.45 or 0.3 mL for normal or hemophilic mouse study,respectively) are drawn into a 1 mL syringe (charged with 50 or 30 μL of3.8% Na-Citrate for normal or hemophilic mouse study, respectively) fromthe inferior vena cava at the indicated time point (one animal persample). Plasma samples are assayed for FVIII concentration using thechromogenic assay method described above. PEGylated PEG6 shows greaterplasma recovery compared to BDD or PEG6 (FIG. 21). PEGylated PEG2 showsgreater plasma recovery compared to BDD (FIGS. 22 and 23).

TABLE 6 PK study summary of PEGylated FVIII showing plasma half-lives inhours. Construct Half-life, hr Species BDD 6.6 Normal Rabbit PEG2 4.8Normal Rabbit PEG2-22 kD PEG 7.5 Normal Rabbit PEG2-43 kD PEG 8.0 NormalRabbit PEG6-12 kD PEG 8.2 Normal Rabbit PEG6-33 kD PEG* 9.6 NormalRabbit PEG6-33 kD PEG 17.4 Normal Rabbit BDD 4.5 Normal Mouse PEG2-22 kDPEG 7.3 Normal Mouse PEG6-12 kD 5.3 Normal Mouse PEG14-33 kD PEG 7.3Normal Mouse PEG14-12 kD PEG 5.5 Normal Mouse PEG22-64 kD 9.2 NormalMouse *Initial prep of 33 kD PEGylated PEG6 with half-life of 9.6 hr inrabbits was not as pure as a later prep that yielded 17.4 hr.

TABLE 7 Plasma recovery of PEGylated PEG muteins in hemophilic mice.Fold- improvement in plasma recovery at 16 hours post-injection comparedto the BDD control performed on the same date is reported. Mutein PEGFold PEG 6 12 kD 2.9 PEG 6 33 kD 2.9 PEG 2+6 33 kD 3.3 PEG 14 33 kD 2.5PEG 2+6 33 kD 4.4 PEG 2+14 33 kD 2.1 PEG22 64 kD 3.2

HEMOPHILIC MOUSE (BDD) FACTOR VIII RECOVERY. The Hemophilic Mouse (BDD)Factor VIII recovery histogram shown in FIG. 24 depicts apharmacokinetic (PK) assessment of the half-life of two species of BDDFactor VIII in a hemophilic mouse assay. This assay was designed tomeasure plasma concentrations of both BDD Factor VIII (referred to inFIG. 24 as “wt” or wild type BDD Factor VIII) and the PEG 2+6 doublePEGylated variant of BDD Factor VIII (and identified elsewhere herein asthe L491C, K1808C double variant of BDD Factor VIII) at three timepoints post intravenous administration in a mouse model. While the PKassessments at both the 0.8 and 4 hour time points were comparable, the16 hour assessment is particularly note worthy. At 16 hours,approximately four times (400%) as much of the doubly PEGylated BDDFactor VIII variant (PEG 2+6) remained in the mouse plasma 16 hoursafter administration as compared to the un-PEGylated molecule.

KIDNEY LACERATION MODEL. To determine if PEGylated FVIII muteins wereefficacious at stopping a bleed in a hemophilic mouse, the kidneylaceration model was employed. Hemophilic mice (C57/BL6 with a disruptedFVIII gene) are anesthetized under isofluorane and weighed. The inferiorvena cava was exposed and 100 ul of either saline or FVIII were injectedusing a 31 gauge needle. The needle was carefully removed and pressureapplied at the sight of injection for 30-45 seconds to prevent bleeding.After two minutes, the right kidney was exposed and held between theforceps along the vertical axis. Using a #15 scalpel, the kidney was cuthorizontally to a depth of 3 mm. To insure a uniform depth of thelesion, kidney was lightly held in the middle to expose equal tissue oneither side of the forceps. The exposed surface of the kidney was cut tothe depth of the forceps. Blood loss was quantified as described above.Different doses of FVIII were tested on mice to characterize the doseresponse relationship of FVIII on kidney bleeding. PEGylated PEG2 showscomparable potency to BDD in reducing blood loss after mouse kidneyinjury (FIG. 25). Thus, although the coagulation activity of PEGylatedPEG2 is lower than that of BDD, this kidney laceration model shows thatthe in vivo efficacy of PEGylated PEG2 was not measurably reducedcompared to BDD, consistent with the chromogenic assay data.

ANTIBODY INHIBITION ASSAY. Adding a high molecular weight polymer suchas polyethylene glycol (PEG) specifically at position 491 (i.e. PEG2)should reduce binding and sensitivity to mAB 413, and by extension to alarge proportion of patient inhibitory antibodies since many patientsdevelop inhibitor antibodies against the same mAB 413 epitope. To testthis, increasing amounts of mAB 413 was incubated with non-saturatingamounts (0.003 IU/mL) of BDD or 43 kD PEGylated PEG2 and tested forfunctional activity in a chromogenic assay (FIG. 26). R8B12, anon-inhibitory antibody, and ESH4, an inhibitory antibody that targetsthe C2 domain were used as controls. PEGylated PEG2 is indeed moreresistant to mAB 413 inhibition than BDD and shows a similar inhibitionpattern in the presence of the control antibodies that do not bind nearthe 491 position. Furthermore, the protection effect of PEG against mAB413 inhibition is dependent on PEG size, with larger PEGs having agreater effect (FIG. 27). To test whether PEGylated FVIII is moreresistant to inhibitor antibodies from patients, chromogenic activitywas measured in the presence of a panel of plasma derived fromhemophilia A patients who have developed inhibitors to FVIII. Of the 8patient plasma tested, 43 kD PEGylated PEG2 was more resistant topatient plasma inhibition than BDD in 4 patient plasma samples. Forexample, PEGylated PEG2, PEG6, or PEG2+6 showed greater residualactivity than BDD in one patient plasma but not in another plasma (FIG.28). The diPEGylated PEG2+6 appears to be more resistant thanmonoPEGylated PEG2 or PEG6. These results suggest that PEGylated PEGmuteins can be more effective in treating patients that developinhibitors to FVIII.

HIGH THROUGHPUT PEGYLATION SCREENING. PEGylation efficiency of aparticular PEG mutein is unpredictable, especially since there is nodirect structural information of BDD. For example, based on thestructure model of BDD, one would predict the PEGylation efficiency ofPEG4 and PEGS should be very high, similar to that of PEG2 and PEG15since all three positions are surface exposed and point outwardlyaccording to the structure. Thus, to use PEG to search for novelclearance mechanism via systematic PEGylation will require a largenumber of muteins to be screened.

To rapidly screen a large number of PEG muteins, a novel high throughputmethod has been developed that can test PEGylation efficiency andfunctional activity of PEGylated products from transiently transfectedmuteins. As little as 5-10 mL of transiently expressed PEG muteins withan FVIII chromogenic value of as low as 0.1-0.2 IU/mL is concentrated byabout 50-fold using Amicon-centra Ultra device MWCO 30K so that theconcentration of FVIII reaches above 1 nM, near the affinity range ofantibody to FVIII interaction. The concentrated PEG mutein (˜300 uL) isincubated with ˜30 uL of C7F7 FVIII antibody resin overnight at 4° C.,washed, eluted, dialyzed, and reduced. The reductant is removed and thereduced PEG muteins is PEGylated and run on a Western analysis asdescribed above (FIGS. 29 and 30). Relative PEGylation efficiency oftransiently expressed PEG muteins matches exactly to that of purifiedPEG muteins.

Dozens of PEG muteins can be screened by this method in one to twomonths. For example, PEG14 (K1804C BDD) had at least about 80%PEGylation of light chain with a 12 kD PEG and no PEGylation of heavychain (data not shown), consistent with the K1804C mutation located onthe light chain. The Ca to CB distance between K1804 and K1808 (PEG6position) is only 8.4 angstrom based on the BDD structure, suggestingthat the introduction of a 43 kD PEG at this position will have similarimprovement in PK as the 33 kD PEGylated PEG6, with the advantage ofmuch higher PEGylation yield. Relative PEGylation yield for all PEGmuteins tested are summarized in Table 8. PEGylation was highlyselective for the particular FVIII chain where the cysteine mutation wasintroduced, in that every mutein with the cysteine in the heavy chainonly gets PEGylated on the heavy chain while every mutein with thecysteine in the light chain gets PEGylated on the light chain. Muteinnumbers 2 to 31 represent cysteine mutations of BDD replacing the nativeamino acid at the position listed with a cysteine. PEG2+6 is a doublemutein of BDD where position 491 and 1808 were substituted withcysteines. A1 and A2, (and B domain for KG-2, the full-length FVIII)belong to the heavy chain while A3, C1, and C2 belong to the lightchain. PEGylation efficiency was estimated from running the PEGylatedproducts on a SDS PAGE comparing the intensities of the PEGylated bandwith unPEGylated band: +++˜>80% PEGylation yield, ++˜30-70% yield,+˜10-30% yield, and −˜<10% yield.

TABLE 8 PEGylation efficiency for various PEGylated FVIII. PEG MuteinPosition Domain H-PEG L-PEG 2 491 A2 +++ − 4 504 A2 + − 5 468 A2 + − 61808 A3 − ++ 7 1810 A3 − ++ 8 1812 A3 − − 9 1815 A3 − − 11 1795 A3 − +12 1796 A3 − + 13 1803 A3 − ++ 14 1804 A3 − +++ 15 377 A2 +++ − 16 378A2 +++ − 17 556 A2 ++ − 20 2118 A3 − + 21 81 A1 ++ − 22 129 A1 ++ − 23422 A2 − − 25 570 A2 − − 26 1864 A3 − ++ 27 1911 A3 − +++ 28 2091 C1 −++ 29 2284 C2 − + 30 711 A2 + − 31 1903 A3 − ++ 2+6  490/1808 A2/A3 +++++ 2+14 490/1804 A2/A3 +++ +++ KG-2 B +++ −

MASS SPECTROMETRY ANALYSIS OF REDUCED PEG MUTEINS. To determine theidentity of the “cap” that prevents direct PEGylation of PEG muteins orfull-length FVIII, PEG2+14 was reduced with TCEP at concentrationsranging from 67 uM to 670 uM. PEGylation yield increased in proportionto increasing amounts of TCEP (FIG. 31). The same samples were alsoanalyzed by mass spectrometry prior to PEGylation (FIG. 32). In order tohave a protein domain that could be directly studied, the samples weredigested with thrombin at a ratio of 20 units/mg FVIII for 30 minutes at37° C. Thrombin cleavage produces an A2 fragment that includes residues372 to 740 and no occupied glycosylation sites. The digested sample wasinjected onto a C4 reversed phase liquid chromatography system and theeluent from the column was introduced directly into the quadrupoletime-of-flight mass spectrometer via an electrospray interface. The massspectrum from under the chromatographic peak corresponding to the A2domain was deconvoluted to provide a protein intact mass value. Prior toreduction, the A2 domain of PEG2+14 yields a mass that is 118 daltonslarger than theoretically predicted. As the TCEP concentration isincreased, a new peak that has the precise predicted mass of A2 domainappears. The proportion of this new peak increases as the TCEPconcentration is increased. The 118 dalton difference can be accountedfor by cysteinylation at residue Cys 491 via disulfide formation with acystine (119 Da) and instrumental accuracy. Thus this shows that the PEGmuteins are capped by a cysteine, which prevents direct PEGylation.

All of the references disclosed herein are hereby incorporated herein intheir entireties.

1.-35. (canceled)
 36. A method for the treatment of hemophilia in apatient who has already developed factor VIII inhibitory antibodiescomprising administering a therapeutically effective amount of apharmaceutical composition of a conjugate having factor VIIIprocoagulant activity comprising a functional factor VIII polypeptidecovalently attached to one or more biocompatible polymers.
 37. Themethod of claim 36, wherein the biocompatible polymer comprisespolyalkylene oxide.
 38. The method of claim 36, wherein thebiocompatible polymer comprises polyethylene glycol.
 39. The method ofclaim 38, wherein the polyethylene glycol comprises methoxypolyethyleneglycol.
 40. The method of claim 39, wherein the methoxypolyethyleneglycol has a size range of from 3 kD to 100 kD.
 41. The method of claim40, wherein the methoxypolyethylene glycol has a size range of from 5 kDto 64 kD.
 42. The method of claim 41, wherein the methoxypolyethyleneglycol has a size range of from 5 kD to 43 kD.
 43. The method of claim36, wherein the biocompatible polymer is covalently attached to thefunctional factor VIII polypeptide at a site that is or is within 20angstrom of a binding site for factor VIII inhibitory antibodies. 44.The method of claim 36, wherein the binding of factor VIII inhibitoryantibodies to the conjugate is less than binding of the antibodies tothe polypeptide when it is not conjugated.
 45. The method of claim 36,wherein the conjugate comprises a functional factor VIII polypeptidecomprising the amino acid sequence of SEQ ID NO: 3 or
 4. 46. The methodof claim 38, wherein the conjugate is monopegylated or dipegylated. 47.The method of claim 38, wherein the conjugate comprises a functionalfactor VIII polypeptide comprising the amino acid sequence of SEQ ID NO:4 or an allelic variant thereof.